Difference between revisions of "Items In Progress"

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'''This page is a place holder for us to put items that will be scheduled for discussion at upcoming meetings.'''  
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'''This page is a place holder for us to put items that are being worked on or under development.'''  
  
 
Please include the date when the item was added;  topics will move off of here as they are dealt with.
 
Please include the date when the item was added;  topics will move off of here as they are dealt with.
  
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-Go back to [[POC_Meetings_Minutes]] main page
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- Go back to [[POC_Meetings_Minutes]] main page
  
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- All new terms and changes should be listed here: [[Release_21]]
  
  
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=Primordia=
 
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These issues came up while we were working on new term requests for Agrinomics.
 
  
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primordium (PO:0025127): A portion of plant tissue that differentiates and develops from meristem tissue into a new plant structure. [source: POC:Curators]
 
  
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Comment: The primordium is the first distinct form in the development of a plant structure.
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=Annotation Guidelines=
 +
Comments from PJ from previous meeting (9-27-11):  
 +
Ask MS if she can write up a small blurb on how she created the Maize annotations.  Maize probe ids => gene ids  methods and cut-offs, a guide for other collaborators and  a page for the info.
 +
Maybe co-author it with SR
  
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leaf primordium: A phyllome primordium that will develop into a leaf. [source: POC:Curators]
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-This will also be helpful when applying for new grants
  
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Comment: Emerges as an outgrowth in the shoot apex (flanking the meristem).
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-it would be helpful to have a detailed guide on our wiki for collaborators
  
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I think we should modify this to say that it develops from the peripheral zone (PO:0000225) and is part of the shoot apex.
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* Need to update the [[Annotation_Association_File_Format]] page
  
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''"The SAM consists of two zones. The cells of the central zone (CZ), which occupy the center of the SAM, are undifferentiated and divide to produce cells in the peripheral zone (PZ), a ring of cells below the CZ (21). Cells in the CZ are unable to form primordia. LPs (leaf primordia) only occur in the PZ."''
+
=Requests from SF- Anatomy terms in progress...=
  
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General question: Do these tissues only occur in the primordium, or continue on after it becomes a young leaf? When does it stop being a primordium? If these tissues are all part of LP, then presumably the LP ends when cell stop dividing. I think usually the term primordium is used for the earliest stage of an organ's development, not all the way up until cell division ceases. Maybe better to say they develop from LP and are part_of leaf during PO:0001052 leaf expansion stage.
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==Request for "rind" or outer layer of a maize or sorghum stem==
  
 +
Request for a term for the outer covering of a maize or sorghum stalk.
  
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''We felt primordium should probably be an organ. All primordia have at least two types of tissue - protoderm and ground meristem(?).''
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[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/596/ link to #596]
  
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''Primordium ends and leaf begins with the formation of the different meristems (adaxial, plate) that contribute to the final form of a leaf.''
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[http://www.sciencedirect.com/science/article/pii/S2090447912000524 structure and properties of sorghum stalks]
  
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''Problem with having different types of primordia as organs means they will all have dual parentage (is_a primordium and is_a whatever type of organ.  We were trying to get rid of that when we made it is_a tissue.''
 
  
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''promeristem as synonym of AM, not RAM''
+
Propsed new terms:
  
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=User requests open on Source Forge; PSDS=
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=='''Abscission Zones'''==
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==from MaizeGDB:==
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June 2014
  
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==[http://sourceforge.net/tracker/?func=detail&aid=3324056&group_id=76834&atid=835555 coleoptile emergence]==
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Added new terms and revised existing:
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This was discussed at the NYBG Meeting, on [[Sunday_Sept_11th,_2011]]
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* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/590/ fruit pedicel abscission zone (PO:0025605)].  Def'n: An abscission zone (PO:0000146) that forms as a swelling or joint on the fruit pedicel (PO:0004536).
  
 +
Ref: http://www.plantphysiol.org/content/158/1/439 (PMID:22106095)
  
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We don't need to deal with all of this before the release, because Mary will use radicle emergence stage instead of coleoptile emergence.
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See also:
 +
* Mao et al., Nature, 2000. JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development 
 +
(http://www.nature.com/nature/journal/v406/n6798/full/406910a0.html)
 +
* Szymkowiak and Irish Plant Cell. 1999. Interactions between jointless and wild-type tomato tissues during development of the pedicel abscission zone and the inflorescence meristem. (http://www.ncbi.nlm.nih.gov/pubmed/9927636?dopt=Abstract)
  
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From MS (MaizeGDB): It would be more useful for maize if the definition for '''coleoptile emergence PO:0007045''' were altered to be: Emergence of coleoptile from the seed. (rather than above ground)
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===New term needed: flower pedicel abscission zone (PO:0025608)===
 +
[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/590/ flower pedicel abscission zone (PO:0025608)]: An abscission zone (PO:0000146) that forms as a swelling or joint on the flower pedicel (PO:009052).
  
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This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.  
+
PMID:24744429
 +
Nakano T, et al.  (2014) The AP2/ERF transcription factor SlERF52 functions in flower pedicel abscission in tomato. Journal of Experimental Botany.
  
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At the POC meeting on [[Sunday_Sept_11th,_2011]], we agreed to keep the existing terms that reference emergence from the soil, but rename them as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.''
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http://jxb.oxfordjournals.org/content/early/2014/04/15/jxb.eru154.full
  
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Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.
+
Added relations:
 +
* flower pedicel abscission zone (PO:0025608) part_of flower pedicel
 +
* fruit pedicel (PO:0004536) develops_from flower pedicel (PO:0009052)
 +
* fruit pedicel abscission zone (PO:0025605) develops_from flower pedicel abscission zone (PO:0025608)
  
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'''current structure:'''
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===Renamed existing term: pedicel > flower pedicel (PO:0009052)===
  
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[[File:germination_stages.jpg]]
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Currently: pedicel (PO:0009052): An inflorescence branch (PO:0009081) that supports an individual flower (PO:0009046) in an inflorescence (PO:0009049).
  
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Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.  
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Renamed: "flower pedicel"  to differentiate it from the fruit pedicel (PO:0004536), which is an infructescence branch.
  
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Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.
+
===Renamed existing term: flower abscission zone > floral organ abscission zone (PO:0006502)===
 +
[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/193/ flower abscission zone (PO:0006502)]:
  
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===current and proposed terms and definitions===
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Was: Zone at base of the flower that contains an abscission (or separation) layer and a protective layer, both involved in the abscission of the flower and its parts.
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'''All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.'''
 
  
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'''current: shoot emergence (PO:0007030):''' Shoot or leaf breaks through the soil surface.
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This was revised as the AZ of a whole flower is different that that of the floral organs (sepals, petals and filaments).
  
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'''proposed: shoot emergence from growth medium development stage (PO:0007030):''' A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the growth medium and ???.  
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Revised name and definition:  
 +
* floral organ abscission zone (PO:0006502): An abscission zone (PO:0000146) at the base of a flower (PO:0009001) where a floral organ (PO:0025395) separates during floral organ abscission (GO:0010227).
  
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Comment: This terms is used only for seed plants.
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Made this part_of a floral organ (PO:0025395), rather than a direct part_of a flower
  
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'''proposed: shoot emergence from seed coat development stage (new number):''' A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the seed coat and ???.
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== New term request: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/589/ microgametophtye development stage]==
  
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Comment: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.
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'''Issue: We have megagametophyte development stage (PO:0007621), but do not have a similar term for microgametophtye development stage.'''
  
 +
Question: how do the megagametophyte development stage (PO:0007621) and proposed microgametophtye development stage (new) fit in with the gametophyte development stage (PO:0028003)?? 
  
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'''current: coleoptile emergence (PO:0007045):''' Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]
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- multicellular plant gametangium (PO:0025124)- a plant organ- children: antheridium (PO:0025125) and archegonium (PO:0025126)
  
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'''proposed: coleoptile emergence from growth medium development stage (PO:0007045):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the growth medium and ???
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- unicellular plant gametangium (PO:0025521): a plant cell- no child terms...
  
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Comment: This terms is used only for seed plants.
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''Currently, megagametophyte development stage (PO:0007621) is_a ovule development stage (PO:0007619), but it should be part_of.''
  
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'''proposed: coleoptile emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the seed coat and ???
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* plant ovule (PO:0020003): A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006).
  
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Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.
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* Moved megagametophyte development stage (PO:0007621) to be is_a gametophyte development stage (PO:0028003). part_of ovule development
 +
** Revised definition: A gametophyte development stage (PO:0028003) during which the megagametophyte (PO:0025279) develops.added dbxref to: OBO_SF2_PO: 589
 +
''This definition should be worked on further, and the child terms need work as well.''
  
 +
* Created new term: microgametophtye development stage (PO:0025602): A gametophyte development stage (PO:0028003) during which a microgametophyte (PO:0025280) develops.
  
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'''current: cotyledon emergence (PO:0007049):''' Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]
+
* pollen development stage (PO:0001007) should be a is_a microgametophtye development stage since pollen is_a microgametophyte (PO:0025280).
  
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'''proposed: cotyledon emergence from growth medium development stage (PO:0007049):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the growth medium and ???
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''Currently pollen development stage (PO:0001007) is_a androecium development stage (PO:0007605)- but it should probably be part_of.''
  
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Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.
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androecium (PO:0009061): A collective phyllome structure (PO:0025023) composed all of the stamens (PO:0009029) in a flower (PO:0009046).
  
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'''proposed: cotyledon emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the seed coat and ???
 
  
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Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination. May occur simultaneously with cotyledon emergence form the growth medium.  
+
* moved pollen development stage (PO:0001007) to be is_a child of the new term: microgametophtye development stage (PO:0025602). part of androecium development stage_ (PO:0007605)
  
 +
Current definition: Stages of development of the pollen defined by characteristic morphological, cytological, histological or other visible features.
  
 +
Revised definition:
 +
pollen development stage (PO:0001007): A microgametophtye development stage (PO:0025602) during which the pollen (PO:0025281) develops.
  
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'''current: epicotyl emergence (PO:0007054):''' Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]
+
''This definition should be worked on further, and the child terms need work as well.''
  
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'''proposed: epicotyl emergence from growth medium development stage (PO:0007054):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the growth medium and ???
+
==caryopsis hull (PO:0006000)==
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/239/ caryopsis hull (PO:0006000)]: A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) and develops from a dried lemma and palea. [source: POC:Ramona_Walls]
 +
** Comment: None
 +
''I think in maize, the hull is actually pericarp tissue, perhaps we should not include the last part.''
  
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Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination.
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==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/575/ founder cells]==
 +
New terms:
 +
phyllome founder cell (PO:0025586)]: A plant cell (PO:0009002) that is part of the phyllome anlagen (PO:0025430).
  
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'''proposed: epicotyl emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the seed coat and ???
+
Comment: As a group, the phyllome founder cells encompass several layers of the shoot apical meristem (PO:0020148) and form a phyllome anlagen (PO:0025430). Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria.
  
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Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination. May occur simultaneously with epicotyl emergence form the growth medium.
+
PMID:12610522
  
 +
vascular leaf founder cell (PO:0025592): A phyllome founder cell (PO:0025586) that is part of a vascular leaf anlagen (PO:0025431).
  
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'''current: hypocotyl emergence (PO:0007043):''' Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]
+
Comment: As a group, the vascular leaf founder cells encompass several layers of the shoot apical meristem (PO:0020148) and form a vascular leaf anlagen (PO:0025431). Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria.
  
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'''proposed: hypocotyl emergence from growth medium development stage (PO:0007043):''' A shoot emergence stage has as a participant a whole plant during the interval between emergence of a hypocotyl from the growth medium and ???
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Revised:  
 +
vascular leaf anlagen formation stage PO:0001003: A vascular leaf initiation stage (PO:0007040) during which the vascular leaf founder cells (PO:0025592) of the shoot apical meristem (PO:0020148) form a vascular leaf anlagen (PO:0025431).
  
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Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.
+
==Revisions to cortex (PO:0005708) and other portion of ground tissue (PO:0025059) children==
  
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'''proposed: hypocotyl emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a hypocotyl from the seed coat and ???
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See notes from discussion on POC call [[POC_Conf._Call_9-24-13]]
  
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Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination. May occur simultaneously with hypocotyl emergence form the growth medium.
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Issue is that some cortex terms are children of cortex (PO:0005708) and others are is_a portion of ground tissue (PO:0025059)
  
 +
[[File:Cortex terms.png]]
  
  
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Could also add terms for feeder emergence for some gymnosperms.
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Fill in details here.....
  
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For all of the above terms, need to check existing synonyms and move or copy them as needed.
 
  
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==[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 tuber growth and development stages]==
+
==New terms Added in Release #20:==
 +
*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ fused perianth (new PO:0025880)]: A perianth (PO:0009058) in which one or more of the petals (PO:0009032), sepals (PO:0009031), and/or tepals (PO:0009033) are fused.
  
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This item has been open on SF since 6/2009
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Comment: The petals (PO:0009032), sepals (PO:0009031) and tepals (PO:0009033) may be fused anywhere along the phyllome margin (PO:0025018). In some cases where the calyx (PO:0009060) and corolla (PO:0009060) are fused at the base it is referred to as a perianth tube.
  
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I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).
+
-Added Narrow synonyms: adnate perianth and connate perianth
  
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Suggested stages:
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*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ fused corolla (new PO:0025581)]: A corolla (PO:0009059) that is composed of fused petals (PO:0009032).
 +
** exact synonym: connate petal structure
  
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-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
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*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ fused calyx (new PO:0025582)]: - A calyx (PO:0009060) that is composed of fused sepals (PO:0025584). 
 +
**Exact synonym: connate sepal structure
  
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-tuber initiation
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*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ fused petal (new PO:0025583)]: - A petal (PO:0009032) that is part of a fused corolla (PO:0025581) or a fused perianth (PO:0025580).
 +
**Comment: In fused perianth (PO:0025580), the fused petal (PO:0025583) may be joined to a fused sepal (PO:0025584) or another fused petal.
  
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-tuber growth
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* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/542/ free petal (PO:0025569)]: A petal (PO:0009032) that is part of a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).
  
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-tuber maturation
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***comment: A free petal (PO:0025569) only occurs in a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583). If you are describing a petal (PO:0009032) that is part of a perianth (PO:0009058) where none of the sepals (PO:0009031) and/or petals (PO:0009032) are fused, you should use petal.
  
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How we work these in will depend on restructuring of PGDSO
 
  
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l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
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*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ fused sepal (new PO:0025584)] - A sepal (PO:0009031) that is part of the fused calyx (PO:0025582) or a fused perianth (PO:0025580).  
  
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=User requests open on Source Forge: PAO=
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*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ free sepal (PO:0025587)]: A sepal (PO:0009031)that is part of a perianth (PO:0009058) that contains fused sepals (PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).
−
==Cacti terms:==
 
−
spinule: word for when the spines are stipules – synonym of stipule spine
 
  
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In Beentje, spinule is defined as a small spine. Could be narrow synonym for stipule spine and other kinds of spines
+
**comment: A free sepal (PO:0025587) only occurs in a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583). If you are describing a sepal (PO:0009031) that is part of a perianth (PO:0009058) where none of the sepals (PO:0009031) and/or petals (PO:0009032) are fused, you should use sepal.
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3438986&group_id=76834&atid=835555 areole]===
+
==Need to look at these associated terms:==
 +
* is_a:
 +
** PO:0025324 : banner petal [0]
 +
** PO:0025326 : keel petal [0]
  
−
Proposed definition: An axillary bud that does not elongate, in which the leaves develop as spine leaves (PO:0025173).
+
* part_of
 +
** PO:0025144 : petal apex [0]
 +
** PO:0025146 : petal base [0]
 +
** PO:0006041 : petal epidermis [0]
 +
** PO:0025008 : petal margin [0]
 +
** PO:0006069 : petal parenchyma [0]
 +
** PO:0025511 : petal spur [0]
 +
** PO:0025218 : petal stomatal complex [0]
 +
** PO:0000054 : petal vascular system [0]
 +
** PO:0025325 : wing petal [0]
  
−
Comment: Found in Cactaceae. Appears as a cluster of spines. May be covered in trichomes. In species with tubercles, the areole is often found at the distal end of the tubercle. The areole originates in the axil of the leaf that becomes the tubercle but is displaced to the tip of a tubercle through adnation (fusion of two organs of different types).
 
  
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is_a axillary bud
+
For corolla:
 +
* part_of: 
 +
** corolla spur PO:0025512: Def'n: A collective organ part structure (PO:0025269) that is a slender, hollow extension of a corolla and has as parts segments of two more fused petals.
 +
''- should be is_a fused corolla?''
 +
 +
** keel PO:0025327: A boat-shaped collective phyllome structure (PO:0025023) that consists of the two lowest petals (PO:0009032) of a papilionaceous corolla (PO:0009059). Comment: The two petals of the keel are often fused at the apex and free at the base. The keel projects toward the front of the flower. Found in the flowers of some Fabaceae.
 +
 +
** PO:0009032 : petal [0]
  
−
ref.: Bell and Bryan, Plant Form
+
* fused corolla (PO:0025581): A corolla (PO:0009059) that is composed of fused petals (PO:0025583).
 +
* calyptra corolla (PO:0025330): A fused corolla (PO:0025581) that is composed of fused petals (PO:0025583). Very similar definitions
  
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===glochid===
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/98/ epicalyx] ==
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3439006&group_id=76834&atid=835555 cladode and phylloclade]===
+
* epicalyx (PO:00090630): A collective phyllome structure (PO:0025023) composed of two or more phyllomes immediately outside the calyx (PO:0009060). [source: POC:curators]
−
From Beentje:
 
  
−
cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf
+
''Do we need a new term for epicalyx bract? - What are the individual members of the epicalyx; they are bracts.''
  
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phylloclade: portion of stem or branch (several nodes an dinternodes) flattened and expanded to serve the functions of a leaf.
+
Existing term: flower bract (PO:0009034): A bract that subtends a perianth that is part of a flower. [source: POC:curators] 
  
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FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
+
''Add epicalyx bract as an exact synonym?, or make a new child of flower bract . Not every flower bract is part of an epicalyx''
  
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proposed definition:
+
''Example from MAG: In the [http://www.plantsystematics.org/imgs/dws/r/Trochodendraceae_Trochodendron_aralioides_26193.html Trocodondraceae], the perianth is completely lacking, but they have little bracts subtending the reproductive structure.
  
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cladode: A shoot axis that is flattened and expanded.
+
''Decided that we needed to add a new term:''
  
−
comment: Has an increased surface area for photosynthesis and may function similar to a leaf in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes.
+
''epicalyx bract (new PO:0025577): A flower bract (PO:0009034) that is part of the epicalyx (PO:0009063). It will be sibling to the existing terms lemma and palea.''
  
−
synonyms: phylloclade, cladophyll
+
==arilloid and arillode and caruncle==
  
−
Need to open a SF tracker for these
+
There is an issue in OE with these that the exact synonyms are the same in Spanish, so it generates an error.''this was resolved in Release #20''
  
−
Should also add 'rib' for cacti and other plants
+
* '''arilloid (PO:0019022)''': A cardinal part of multi-tissue plant structure (PO:0025498) that is a fleshy outgrowth of a seed (PO:0009010). [source: ISBN:9780881928501]
 +
Comment: Often conspicuous and found on seeds with a hard testa that are dispersed by animals. There is some variation in how different sources define the subtypes of arilloids.
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]==
+
Synonyms narrow: arillode; exact: ariloide (Spanish)
 +
   
 +
* '''arillode (PO:0025378)''': An arilloid that is an elaborate outgrowth of a seed at the micropyler end. [source: ISBN:9780881928501]
 +
Comment: Generally larger than a caruncle and not hard.
  
−
Submitted by Rich Zobel (Nov 2009).
+
Synonyms exact: ariloide (Spanish)
  
−
Still need to work on definitions for these terms.
+
*'''caruncle (PO:0020060)''': An arilloid that is an outgrowth of a seed next to the micropyle. [source: ISBN:9780881928501]
 +
Comment: Often hard and generally smaller and less elaborate than a arillode.
  
−
=Vascular tissues and cell types=
+
Synonyms exact: carúncula (Spanish)
  
−
THIS PART IS STILL UNDER CONSTRUCTION
+
*aril PO:0009090: An arilloid that is an outgrowth of a seed from a seed funicle. [source: ISBN:9780881928501]
  
−
These terms will need to be fixed before the Wood Ontology meeting in February.
+
Synonyms
 +
exact: arilo (Spanish)
 +
exact: 仮種皮 (Japanese)  
  
−
==vascular tissue types==
+
Comment : Usually envelopes most of the seed and is fleshy. If the ovule is pressed against the funicle to form a raphe, it may appear that the aril is growing from the raphe.
  
−
For vascular plants, we have the class:
+
==[http://sourceforge.net/tracker/?func=detail&aid=3609179&group_id=76834&atid=835555 floral node]==
  
−
'''portion of vascular tissue (PO:0009015):''' A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]
+
suggested definition: A cardinal organ part of a shoot axis where one or more flower may arise
  
−
Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.
+
Parent/relationship: is_a shoot node (PO:0005004)
  
−
part_of vascular bundle (which is part_of vascular system)
+
Submitted: Johnny Lloyd
  
−
This is okay, but suggest that we change definition to include xylem '''or''' phloem, and it may not always be part_of vascular bundle.
 
  
 +
inflorescence node:  A shoot node that is part of an inflorescence axis and where a spikelet, flower, floret or inflorescence branch is attached. [source: GR:Pankaj_Jaiswal]. 
 +
PO:0006325
  
−
'''Proposed definition:''' A portion of plant tissue that has as parts tracheary elements or sieve elements.
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/535/ spine petiole]==
  
−
Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or as scattered vascular bundles. May include other types of tissues or cells, such as parenchyma or fibers.
+
Requested by DWS: spine petiole (new PO:id)- A petiole that is sclerified and persistent.
  
−
part_of vascular system (should add vascular system participates_in sporophytic phase)
+
The petiole abscisses longitudinally and the blade withers.
  
 +
See the photo and description on this page: [http://waynesword.palomar.edu/ecoph30a.htm "Spines From Modified Petioles"]
  
−
'''vascular bundle (PO:0005020) current def.:''' A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]
+
==[http://sourceforge.net/tracker/?func=detail&aid=3609178&group_id=76834&atid=835555 adventitious branch]==
  
−
This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.
 
  
−
'''proposed definition:''' A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.
+
Definition: A shoot axis (PO:00025029) that develops in an unusual place
  
−
Comment: Usually contains both xylem and phloem. May also contain other types of cells or tissue such as fibers, vascular cambium, or portions of ground tissue.
+
Parent/relationship: is_a shoot axis (PO:0025029), develops from an adventitious bud
  
−
part_of vascular system
 
  
−
add vein as exact synonym -- can be in any organ
+
adventitious shoot axis
  
−
===primary and secondary vascular tissue===
+
==shoot-borne root (PO:0000042)==
−
'''primary vascular tissue:''' A portion of vascular tissue that develops from a procambium. (ref: Esau)
+
synonym: adventitious root
  
−
comment: Forms as part of primary growth (GO:xxxx).
+
Need to align these three with the shoot-borne root
 +
* adventitious root apical meristem ; PO:0006021
 +
* adventitious root epidermis ; PO:0006039
 +
* adventitious root nodule ; PO:0000040
  
−
'''secondary vascular tissue:''' A portion of vascular tissue that develops from a vascular cambium. (ref: Esau)
+
==leaf lamina PO:0020039==
 +
-fix typo in comment
 +
 +
*Def'n: A phyllome lamina (PO:0025396) that is the part of a leaf (PO:0025034) exclusive of the petiole (PO:0020038) or leaf sheath (PO:0020104), if either is present. 
  
−
comment: Forms as part of secondary growth (GO:0080117) in vascular plants. Often differentiated into the axial system and ray system.
+
*Comment: A leaf lamina is usually dorsiventrally flattened, but may be flattened in a median '''plant''' (perpendicular to the axis) in the case of phyllodes (PO:0025335) or other ensiform leaves (PO:0025333). This term should not be used for leaves that are not laminar (flat), like round leaves in Allium or needle-like leaves in Pinus or some Proteaceae.  
  
−
If we '''set both of these up as a cross products''', then primary and secondary xylem and phloem will be inferred children.
+
If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
  
−
===phloem===
 
  
−
'''phloem (PO:0005417) current def.:''' A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/521/ Ultimate Unit (UU)]==
 +
Requested by: Corvez Adele  Created: 2013-02-01
  
−
'''proposed definition:''' A portion of vascular tissue that has as parts sieve elements.
+
* Ultimate units are last branching-orders inserted at extremities of lateral branching systems. Each unit can divide several times, they are mostly tridimensional and their last dichotomies form ultimate appendages.
 +
Corvez et al., 2012
  
−
Comment: Functions in the conduction of organic substances in vascular plants.
+
suggested parentage: Ultimate unit is_a cardinal organ part
  
−
''Note: currently, sieve element is listed as a synonym of sieve tube member, but this does not correctly follow Esau's usage. It was okay when we only had angiosperms in PO, but is no longer valid. Suggest we make a new term for sieve element, rather than have it as synonym. See below under conductive_and_related_cell_types.''
+
==moss capsule==
 +
need to open tracker for this: [https://sourceforge.net/tracker/?func=detail&aid=3140824&group_id=76834&atid=835555 moss capsule]
  
 +
==[http://sourceforge.net/tracker/?func=detail&aid=3597966&group_id=76834&atid=835555 prothallial cell] and prothallium ==
  
−
'''metaphloem (PO:0006076) current def.:''' Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.
+
On the POC POC call (12-11-12), we identified that we needed to add this as part of the gymnosperm pollen.
  
−
'''proposed definition:''' A portion of primary phloem that differentiates after the protophloem.
+
prothallial cell (PO:0025533):
  
−
Comment: Differentiates before the secondary phloem, if any is formed.
+
proposed def'n: A vegetative plant cell (PO:0009002) that develops from the division of the microspore (PO:0020048) and is part of the microgametophyte of vascular plants other than angiosperms.
  
 +
''should add the PO id for microgametophyte (PO:0025280) to the definition''
  
−
'''protophloem (PO:0006077) current def.:''' The first-formed elements of the primary phloem.
 
  
−
'''proposed definition:''' A portion of primary phloem tissue that has as parts the first-formed sieve elements of the primary phloem.
+
For reference about prothallial cells in gymnosperms see:  
  
 +
Morphology of gymnosperms, by John M. Coulter and Charles J. Chamberlain. pages 2277-278 and 339-340.
  
−
'''primary phloem (PO:0006075) current def.:''' A portion of phloem tissue of the primary plant body.
+
Available online: [http://babel.hathitrust.org/cgi/pt?id=mdp.39015052524801;seq=356;view=1up;num=340 Coulter + Chamberlain, 1910]
  
−
'''proposed definition:''' A portion of phloem tissue that develops from the procambium.
 
  
−
Comment: Primary phloem develops as part of GO:xxxx primary growth. (''see below'')
+
Note: prothallium is a synonym for thallus (PO:0030027) and ....
  
−
develops_from PO:0025275 procambium
+
How does prothallial cell compare to microgametophyte vegetative cell?
  
 +
prothallial cell (PO:0025533):
 +
current def'n: A vegetative plant cell (PO:0009002) that develops from the division of the microspore (PO:0020048) and is part of the microgametophyte of vascular plants other than angiosperms.
  
−
'''secondary phloem (PO:0005043) current def.:''' A portion of phloem tissue formed by the activity of the vascular cambium.
+
Revised: A native plant cell (PO:0025606) which is vegetative and develops from the division of the microspore (PO:0020048) of vascular plants other than angiosperms.
  
−
'''proposed definition:''' A portion of phloem tissue that develops from the vascular cambium.
+
Revised comment:
 +
The prothallial cell (PO:0025533) is part of the microgametophyte (PO:0025280) and is believed to be the remnant of the vegetative tissue of the male gametophyte.
  
−
Comment: Secondary phloem develops as part of GO:0080117 secondary growth.
+
==[https://sourceforge.net/tracker/?func=detail&aid=3080945&group_id=76834&atid=835555 common primordium]==
 +
This request was made by Elena Kramer during the beta review: , I wondered if there was some way to incorporate ...the phenomenon of common primordia (...would only apply to the development ontology)
  
−
develops_from PO:0005598 vascular cambium
+
"During floral development (at least in peas, maybe others), petals and stamens (and maybe other floral organs) may share a common primordium before development of a distinct petal or stamen primordia. We may want to add this to the flower developmental stage branch of the PGDSO."
  
−
===xylem===
+
This could be a structure in the PAE branch, and we can consider adding it as a stage when we work on flower development stages.
  
−
'''xylem (PO:0005352) current def.:''' A portion of vascular tissue composed of xylem elements.
+
''We all agreed that this should be a PAE, rather than a development stage. Need to propose definition on SF.''
  
−
comment: The principal function is the upward translocation of water and solutes. See also primary xylem and secondary xylem.
+
==[https://sourceforge.net/tracker/?func=detail&aid=3082379&group_id=76834&atid=835555 nucellar projections]==
  
−
'''proposed definition:''' A portion of vascular tissue that has as parts tracheary elements.
+
The current definition of nucellar projection (PO:0008007) is: A portion of plant tissue that is the morphologically distinct portion of the nucellus overlying the vascular strands in the grass caryopsis. part_of nucellus.
  
−
comment: Functions in the translocation of water and solutes from roots to the shoot system and in support.
+
''This definition is specific to grasses, and should be rephrased, so it is more general.''
  
 +
Actually, I can't find any references to this outside grasses, so perhaps it is fine as is. Does anyone know of an example of this outside grasses? Maybe in other monocots?
  
−
'''primary xylem (PO:0005849) current def.:''' A portion of xylem tissue of the primary plant body. [source: GR:Pankaj_Jaiswal, ISBN:0122151704, ISBN:0471245194]
+
''No one know of an example outside grasses, so it is okay, but we can rephrase slightly to make it more braod.''
  
−
Comment: In stem or root it is differentiated behind the apical meristem.
+
proposed def.: A portion of plant tissue (PO:0009007) that is a morphologically distinct part of a nucellus (PO:0020020) overlying the vascular bundles (PO:0005020).
  
−
'''proposed definition:''' A portion of xylem tissue that differentiates from the procambium.
+
comment: Found a caryopsis in Poaceae.  
  
−
Comment: Primary xylem develops as part of GO:xxxx primary growth.
+
part_of nucellus
  
−
develops_from PO:0025275 procambium
+
==[https://sourceforge.net/tracker/?func=detail&aid=3205381&group_id=76834&atid=835555 rosette leaf and cauline leaf]==
 +
The definitions for these terms need revision, especially cauline leaf. Rosette leaf is okay, but should be converted to genus-differentia form.
  
 +
'''Current definitions:'''
  
−
'''protoxylem (PO:0000272) current def.:''' A portion of xylem tissue composed of any of the first formed elements of the primary xylem. [source: ISBN:047125208]
+
'''rosette leaf (PO:0000014):''' One of multiple leaves borne in a rosette - a group of leaves, generally borne at the base of the plant, that are separated by very short internodes.
  
−
'''proposed definition:''' A portion of primary xylem that has as parts the first formed xylem elements of the primary xylem.
+
comment: Arabidopsis, vegetative development is characterized by the production of the rosette leaves.
  
 +
'''cauline leaf (PO:0000013):''' Leaf or pairs/whorls of leaves borne on the stem.
 +
Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.
  
−
'''metaxylem (PO:0000372) current def.:''' A portion of xylem tissue that is part of the primary xylem and differentiates after the protoxylem and before the secondary xylem, if any of the latter is formed. [source: ISBN:047125208]
+
comment: In Arabidopsis, refers to the leaves that are borne on ''the elongated inflorescence branches''.
  
−
'''proposed definition:''' A portion of primary xylem that differentiates after the protoxylem.
 
  
−
Comment: Differentiates before the secondary xylem, if any is formed.
+
Perhaps we should use the appropriate growth stages in their definitions,
 +
e.g., PO:0007113 rosette growth, and PO:0007089 stem elongation. However, stem elongation is defined as a vegetative growth stage, so it doesn't really apply to plants that are bolting
  
 +
'''proposed definitions'''
  
−
'''secondary xylem (PO:0005848) current def.:''' A portion of xylem tissue that develops from a vascular cambium. [source: ISBN:0471245194, POC:Curators]
+
'''rosette leaf:''' A vascular leaf (PO:0009025) that is part of a collective leaf structure (PO:0025022) in which the leaves are borne on a stem base (PO:0008039) that has very short stem internodes (PO:0020142).
  
−
Comment: Absent in some dicots and most monocots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas.
+
comment: In many species, including Arabidopsis thaliana, the sporophyte vegetative stage (PO:0007134) is characterized by the production of the rosette leaves.
  
−
Existing definition is okay.
 
  
−
New comment: Secondary xylem develops as part of GO:0080117 secondary growth. Found in gymnosperms and most dicots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas. May be organized into axial and ray systems. Some monocots have a primary peripheral thickening meristem, located near shoot apical meristem, that gives the appearance of secondary growth and may produce lignified tissue that appears woody, but is not composed of secondary xylem.
+
'''cauline leaf (PO:0000013):''' A vascular leaf (PO:0009025) that is borne on a stem (PO:0009047) or  branch (PO:0025073) that has elongated shoot internodes (PO:0005005).
  
−
develops_from PO:0005598 vascular cambium
+
comment: In species that undergo bolting, such as Arabidopsis thaliana, cauline leaves may start to develop before or after the shoot axes elongates.
  
 +
Question: Are there ever cauline leaves forming on an inflorescence axis (PO:0020122)?
  
−
''Note: exarch, endarch, mesarch are descriptors for different types of xylem development.''
 
  
 +
Links from Lol:
  
−
'''tracheid bar (PO:0019026) current def.:''' A distinct ring-like structure, composed of tracheid cells, which surrounds the hilum of some taxa e.g., Phaseolus, and forms a groove in the surface of the pericarp (immediately adjacent to the hilum). [ISBN:0080280293]
+
http://www.arabidopsis.org/portals/education/growth.jsp
  
−
'''proposed definition:'''  A portion of xylem tissue that is a distinct ring-like structure, composed of tracheid cells, which surrounds the hilum and forms a groove in the surface of the pericarp immediately adjacent to the hilum.
+
http://www.jstor.org/stable/2656849
 +
===non-vascular rosette leaves?===
 +
At the POC meeting on 6/7/11, PJ suggested that we make new general terms
 +
for rosette leaf and cauline leaf, is_a children of leaf. Then we could
 +
make specific terms for vascular rosette leaf and vascular cauline leaf.
  
−
Comment: Found some taxa such as Phaseolus. [ISBN:0080280293]
+
However, I don't know if the terms rosette leaf and cauline leaf are ever used for
 +
non-vascular plants. Certainly leaves occur on a stem in mosses and
 +
liverworts, but it is not the case that the leaves first form during a
 +
rosette stage then the stem elongates. Instead, leaves are formed from the
 +
stem apex as it elongates.
  
−
part_of seed; adjacent_to hilum
+
If rosette leaf and cauline leaf only have one child each (vascular rosette
 +
leaf or vascular cauline leaf), is there really a point in making the
 +
general category?
  
−
===leaf vein, midrib, costa===
+
''Don't need these''
  
−
*'''leaf vein (PO:0020138), current def:''' A strand of vascular tissue in the leaf blade.
+
==[https://sourceforge.net/tracker/?func=detail&aid=3299941&group_id=76834&atid=835555 sporocyte]==
 +
'''Existing definitions:'''
  
−
is_a portion of vascular tissue; part_of leaf vascular system
+
'''sporocyte (PO:0006204):''' A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) spores.
  
 +
'''microsporocyte (PO:0020047):''' A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) microspores. [source: ISBN:0878934030]
  
−
'''proposed definition, leaf vein (PO:0020138):''' A vascular bundle that is part of a leaf lamina in a vascular leaf.
+
synonyms: microspore mother cell, PMC, pollen mother cell
  
−
part_of leaf vascular system, part_of leaf lamina
+
'''megasporocyte (PO:0000431):''' A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores. [source: ISBN:0471245208]
  
−
synonym: leaf vascular bundle
+
synonyms: megaspore mother cell, MMC
  
  
−
Suggest new term '''primary leaf vein''': A leaf vein that originates from the base of a leaf lamina  where it attaches to the petiole or to the shoot axis if no petiole is present.
+
At the POC meeting on 5/6/11, we agreed to add sporocyte develops_from archesporial cell.
  
−
Comment: A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139).
+
Already have:
  
 +
megasporocyte develops_from female archesporial cell
  
−
*'''midvein (PO:0020139):''' The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary]
+
microsporocyte dvelops_from primary sporogenous cell, which develops_from male archesporial cell
  
−
Since midvein is_a leaf vein, it should say just "leaf" instead of "leaf or leaf-like organ.
 
  
−
'''proposed definition:''' A primary leaf vein that is the central vein of a vascular leaf.
+
'''Proposed definitions:'''
  
−
Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf.
+
'''sporocyte (PO:0006204):''' A plant cell (PO:0009002) that develops from an archesporial cell (PO:0030056) and undergoes meiosis (GO:0007126) to produces four plant spores (PO:0025017).
  
−
broad synonyms: mid rib, midrib, mid-rib, vascular leaf midvein
+
Add: sporocyte develops_from archesporial cell
  
−
related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128
+
Should we add spore develops_from sporocyte? ''yes''
  
−
We already have terms for secondary, tertiary, quaternary, and higher order veins.
+
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007126 meiosis (GO:0007126)]
  
−
===Primary and secondary growth, lateral meristems, etc.===
 
−
====proposed terms for GO====
 
−
'''primary growth (new term):'''
 
  
−
'''proposed definition:''' Growth of a plant structure from the time of its initiation by an apical meristem until its expansion is completed. Ref: Esau (ISBN:0471245208 or 9780471245209)
+
'''microsporocyte (PO:0020047):''' A sporocyte (PO:0006204) that develops from a primary sporogenous celll (PO:0006088) and undergoes meiosis (GO:0007126) to produces four microspores (PO:0020048). [source: ISBN:0878934030]
  
−
comment: Has its inception in the apical meristems and continues in their derivative meristems - protoderm and procambium - even in older tissues. Primary and secondary growth can occur simultaneously in the same organism.
+
synonyms: microspore mother cell, PMC, pollen mother cell
  
−
is_a growth (GO:0040007)
+
Should we add microspore develops_from microsporocyte?
  
 +
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007140 male meiosis (GO:0007140)]
  
−
'''secondary or lateral growth'''
+
''Better to use meiosis, rather than male meiosis.''
  
−
GO currently defines secondary growth as: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290 
 
  
−
Secondary growth from the vascular cambium does not occur in monocots, but there is a secondary thickening meristem that may be discontinuous from apical meristem that can contribute to another kind of secondary growth. See paper by [http://www.jstor.org/stable/10.2307/4354165 Rudall et al.] in Botanical Review.
+
'''megasporocyte (PO:0000431):''' A sporocyte (PO:0006204) that develops from a female archesporial cell (PO:0006015) and undergoes meiosis (GO:0007126) to produces four megaspores (PO:0020019). [source: ISBN:0471245208]
  
−
Perhaps GO should have a general term for '''lateral growth''' (to mirror PO, see below), with specific subtypes for growth from the vascular cambium and growth from other types of lateral meristems.
+
synonyms: megaspore mother cell, MMC
  
 +
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007143 female meiosis (GO:0007143)]
  
−
'''lateral growth (GO:new term):''' Growth of a plant axis (shoot axis or root) that originates from a lateral meristem (PO:0020145).
+
''Better to use meiosis, rather than female meiosis.''
  
−
Comment: Includes thickening of plant axes due to the activity of a cambium (secondary growth, found in most gymnosperms and dicotyledons), a primary thickening meristem (found in many monocotyledons, some ferns and some cycads), or secondary thickening meristem (in some monocotyledons).
 
  
 +
'''Also need to address:'''
  
−
'''proposed new def., secondary growth (GO:0080117):''' Lateral growth of a plant axis (shoot axis or root) that is an increase in thickness resulting from formation of secondary vascular tissues by the vascular cambium (PO:0005598). Ref: Esau (ISBN:0471245208 or 9780471245209)
+
'''primary sporogenous cell (PO:0006088), current def.:''' It is formed by the division of the male archesporial initial. After several mitotic divisions these cells differentiate into pollen mother cells.
  
−
Comment: Occurs in vascular plants, including gymnosperms and most dicotyledons. Commonly supplemented by activity of the cork cambium (phellogen). Monocotyledons do not have secondary growth, but may undergo primary thickening (GO:xxx) or secondary thickening (GO:xxx), which can give the appearance of secondary growth. Primary and secondary growth can occur simultaneously in the same organism.
 
  
−
Add synonym "cambial secondary growth", which is makes the meaning clearer.
+
'''proposed def.:''' A plant cell (PO:0009002) that develops from a male archesporial cell (PO:0006014) and, after several mitotic divisions, develops into microsporocytes (PO:0020047).
  
 +
''okay''
  
−
'''secondary thickening (GO:new term):''' Lateral growth of a plant axis (shoot axis or root) that is an increase in thickness resulting from formation of tissue from a secondary thickening meristem (PO:xxxx).
 
  
−
comment: Occurs shoot axes in some monocotyledons such as Dracaena, and rarely in roots of monocotyledons. Distinct from primary thickening, because it is distant from and generally discontinuous with the apical meristem.
+
''Note: external ontology ids should go in both the definition and as a Dbxref, because they don't work as links otherwise. They work as links okay in the comments.''
  
−
References: Fahn 1990, ISBN:0080374903, Rudall 1991, JSTOR:4354165
+
==[https://sourceforge.net/tracker/?func=detail&aid=3405173&group_id=76834&atid=835555 spikelet]==
 +
At the POC meeting on 8-30-11, we decided that this definition needs some work.
  
 +
Current def.: Ultimate and congested inflorescence branch of the grasses. [source: APWeb:Glossary]
 +
Comment: It consists of one to many closely-packed flowers and associated glumes etc.
  
−
'''primary thickening (GO:new term):'''  Lateral growth of a plant axis (shoot axis or root) that is an increase in thickness resulting from the activity of a primary thickening meristem (PO:0005039)  
+
Should make it more general, because spikelets are found throughout the Poales (close relatives of grasses).
  
−
comment: Occurs in shoot axes and rarely in roots in many monocotyledons.
 
  
−
Ref: JSTOR:4354165, Rudall 1991, and Esau ISBN:0471245208
+
Proposed def.: A second order inflorescence that has as parts the glumes, a firinflorescence branches with short internodes, and a florets.
  
 +
Comment: Part of a spike type inflorescence as found in grasses and other Poales.
  
−
'''diffuse secondary thickening (GO:new term)''': Lateral growth of the older parts of a stem that occurs when the central parenchyma cells and the not yet fully differentiated fibers of the bundle sheaths continue to undergo cell division and expansion for a long period of time, leading to an increase in girth of the stem.
+
From Ale:
  
−
comment: Occurs in the stems of some Arecaceae (palms).
+
spike: an unbranched, elongated inflorescence with sessile or subsessile flowers or spikelets maturing from the bottom upwards
  
−
Ref.: Fahn 1990, ISBN:0080374903
+
spikelet: a small spike or secondary spike; the ultimate flower cluster of grasses and sedges, consisting of one to may flowers subtended by two bracts (glumes)
  
−
====PO terms for lateral meristems====
+
==[https://sourceforge.net/tracker/?func=detail&aid=3438986&group_id=76834&atid=835555 lamina areole]==
 +
Propose new definitions:
  
−
The PO has a general term for lateral meristem, of which cambium is a subtype:
+
'''phyllome lamina areole (PO:0025391):''' A cardinal organ part (PO:0025001)
 +
that is part of a phyllome lamina (PO:0025396) and is completely surrounded
 +
by phyllome lamina veins (PO:0025348) and cannot be divided into any
 +
smaller parts that are completely surrounded by phyllome lamina veins.
  
−
[[File:lateral_meristem1.jpg]]
+
Comment: Any order of phyllome lamina vein can form the sides of a phyllome
 +
lamina areole. Taken together, the phyllome lamina areoles form a
 +
contiguous field of polygons over the area of a phyllome lamina.
 +
part_of phyllome lamina
  
−
'''lateral meristem (PO:0020145)'''
 
  
−
'''current def.:''' A meristem containing cells along the stem or root that first differentiate and function as members of a mature tissue system but then again take up meristematic activity.
+
'''leaf lamina areole (PO:0025392):''' A phyllome lamina areole (PO:0025391) that
 +
is part of a leaf lamina (PO:0020039) and is completely surrounded by leaf
 +
lamina veins (PO:0020138) and cannot be divided into any smaller parts that
 +
are completely surrounded by leaf lamina veins.
  
−
'''proposed def.:''' A meristem located parallel to the circumference of a plant organ.
+
Comment: Any order of leaf lamina vein can form the sides of a leaf lamina
 +
areole. Taken together, the leaf lamina areoles form a contiguous field of
 +
polygons over the area of a leaf lamina. Free ending veinlets (PO:0025390)
 +
may be found within a leaf lamina areole.
 +
part_of leaf lamina
  
−
comment: Participates in lateral growth (GO:xxxx) of a plant organ, primarily shoot axes and roots. Contrast with apical meristem (PO:0020144).
+
==ovuliferous scale==
 +
New term to add, needed for definition of ovuliferous scale ovule (PO:0025491).
  
 +
"Ovuliferous scale" seems to be the more commonly used name.
  
−
'''root lateral meristem (PO:0006308)'''
+
'''proposed def., ovuliferous scale:''' A megasporophyll (PO:0009027) that is part of a seed-scale complex (PO:id).
  
−
'''current def.:''' Meristem of the root located parallel to the sides of the axis.
+
Comment: Has as part an ovuliferous scale ovule (PO:0025491) and is part of a ovulate cone ().
  
−
comment: Generally causes root thickening. Not to be confused with lateral root meristem, which is the meristem of the lateral root.
+
''need to review this''
  
−
This is just a cambium in the root, which also has vascular cambium and phellogen.
+
''Currently, ovuliferous scale is a narrow synonym of [http://dev.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0009027&session_id=4901b1372716379 megasporophyll]''
  
−
'''proposed new name and def.: root cambium:''' A cambium that is part of a root.
 
  
−
This terms has six annotations. These should be checked, because it is not obvious what some of them have to do with roots.
 
  
−
If we are going to have this term, maybe we should have root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium?
+
'''ovulate cone, new term:''' A strobilus (PO:0025083) that has as parts ovuliferous scales () but no microsporophylls (PO:0009028).
  
 +
synonym: female cone (related)
  
−
'''cambium (PO:0005597)'''
+
''Move more specific synonyms form strobilus to these terms.''
  
−
'''current def.:''' A lateral meristem, the cells of which divide mostly periclinally. [source: ISBN:0080374913]
+
'''microsporangiate cone, new term:''' A strobilus (PO:0025083) that has as parts microsporophylls (PO:0009028) but no megasporophylls (PO:0009027).
  
−
'''proposed def.:''' A lateral meristem that has a part a single layer of cambial initial cells and their derivatives, arranged orderly in radial files.  (Ref.: Esau)
 
  
−
comment: This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599).
+
'''seed-scale complex''': A reproductive shoot system (PO:0025082) that is part of an ovulate cone (PO:0025083) and has as parts a ovuliferous scale () and a ovuliferous scale sterile bract ().
  
  
−
'''vascular cambium (PO:0005598)'''
+
'''ovuliferous scale sterile bract''': A bract (PO:0009055) that is part of a seed-scale complex and subtends an ovuliferous scale ().
  
−
'''current def.:''' A lateral meristem, the cells of which give rise to secondary xylem and phloem, leading to an increase in girth.
+
===Definitions of megasporophyll and microsporophyll===
 +
move part about angiosperms to the comment
  
−
Current definition is okay, but needs minor changes.  
+
Current def., megasporophyll: A structure upon which (or in the axil of which) one or more megasporangia are borne; in flowering plants, a carpel.
  
−
'''proposed def.:''' A cambium that gives rise to secondary xylem and secondary phloem.
+
Current def., microporophyll: A structure on which one or more microsporangia are borne; in flowering plants, the stamen.
  
−
comment: Vascular cambium is located between the secondary xylem and secondary phloem and gives off cells in both directions by periclinal division, leading to an increase in girth of a plant axis.
+
==pericarp and seed coat==
 +
''What is the problem with pericarp?''
  
 +
* open tracker for pericarp cell types for PJ: "There are a number of pericarp components which may need PO terms".
 +
see: http://www.relata.info/docs/RT%202008%201.pdf
  
−
'''cork cambium/phellogen (PO:0005599)'''
 
  
−
'''current def.:''' Lateral meristem which produces the phellem (cork) and the phelloderm.
 
  
−
'''proposed def.:''' A cambium that is part of a periderm and produces phellem (cork) and phelloderm.
+
pericarp (PO:0009084):A wall of a fruit, developed from the ovary or carpel wall.
  
−
comment: Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis.
+
Synonyms related: fruit peel, fruit rind
  
 +
New def.: ''A portion of plant tissue that develops form the ovary wall and forms the outer layer or layers of a fruit.''
  
−
'''primary thickening meristem (PO:0005039)'''
+
comment: ''Usually has as parts an exocarp, mesocarp and endocarp. In a caryopsis, the pericarp is fused with the seed coat.''
  
−
'''current def.:''' A meristem that develops from a peripheral zone of a shoot apical meristem and is responsible for the primary increase in thickness of a shoot axis.
+
endocarp ; PO:0009086, synonym inner epidermis of pericarp
  
−
comment: May appear as a distinct mantle like zone. Often found in monocotyledons.
+
exocarp ; PO:0009085 synonyms outer epidermis of pericarp,
  
−
Esau defines it as originating in the apical meristem, but Rudall's review shows that in some species, it is discontinuous with the SAM.
 
  
−
'''proposed def.:''' A lateral meristem that has a parts multiple layers of cells located near the shoot apical meristem.
+
seed coat: A portion of plant tissue that is the covering of a seed derived from ovular - mainly integumentary - tissue.
  
−
comment: Contributes to primary thickening of the stem, adventitious root formation, and formation of linkages between the stem, leaf, and root vasculature. Contiguous with the shoot apical meristem in some species, but not all. Produces more or less distinct vascular bundles surrounded by ground tissue, as opposed to the more or less continuous xylem and phloem produced by a vascular cambium. A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.
+
Revised: A portion of plant tissue that develops from an integument and forms the covering of a seed. develops_from integument
  
 +
Get rid of "usually" in def. of integument.  From: http://en.wikipedia.org/wiki/Caryopsis
  
−
'''secondary thickening meristem (new term)'''
+
is a type of simple dry fruit — one that is monocarpelate (formed from a single carpel) and indehiscent (not opening at maturity) and resembles an achene, except that in a caryopsis the pericarp is fused with the thin seed coat.
  
−
'''proposed def.:''' A lateral meristem has a parts multiple layers of cells in a shoot axis...
+
The caryopsis is popularly called a grain and is the fruit typical of the family Poaceae (or Gramineae), such as wheat, rice, and corn.
  
−
comment: Contributes mainly to formation of the body of a stem, but may also produce adventitious roots. May be continuous or discontinuous with the primary thickening meristem. Found in some monocot species of the Liliales and Asperigales.
+
The term grain is also used in a more general sense as synonymous with cereal (as in "cereal grains", which include some non-Gramineae). Considering that the fruit wall and the seed are intimately fused into a single unit, and the caryopsis or grain is a dry fruit, little concern is given to technically separating the terms "fruit" and "seed" in these plant structures. In many grains, the "hulls" to be separated before processing are actually flower bracts.
  
 +
link to a more scientific source :http://www.jstor.org/stable/10.2307/2442251
  
  
−
'''Other types of lateral meristems'''
+
we also have the term:
  
−
PO has the terms shoot lateral meristem (PO:0006344), inflorescence lateral meristem (PO:0009105), ear lateral meristem (PO:0009110) and tassel merristem (PO:0009107), plus their subtypes.
+
caryopsis hull (PO:0006000): A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) and develops from a dried lemma and palea. [source: POC:Ramona_Walls]
  
−
Shoot lateral meristem is okay, but inflorescence lateral meristem and all the others are misleading. Inflorescence branches generall develop from apical meristems, not a lateral meristem.
+
==ovary and the like==
 +
An ovary is either the basal part of a carpel (in an apocarpous gyneocium) or the basal part of a syncarpous gynoecium. This is how it is defined in Esau, Raven, Weberling, etc.  
  
−
There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem.  
+
The same can be said of a style or a stigma. Therefore, all of these can be either part_of carpel or part_of gynoecium (which means they are always part_of gynoecium).
  
−
'''inflorescence lateral meristem (PO:0009105)'''
 
  
−
'''current def.:''' The meristem which gives rise to the lateral structures of the inflorescence and contributes to their apical growth.
+
'''ovary wall:''' Part_of ovary, which may be part of carpel or part of gyneocium. Not a valid COP.
  
−
This should be called '''inflorescence branch meristem''', and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.
+
'''style:''' (Raven: A slender column of tissue that arises from the top of an ovary and through which the pollen tube grows). Just like ovary, it may be part of a carpel or part of a group of fused carpels. Weberling uses "monocarpellary style" for a style of a single carpel and "polycarpellary style" for the style of fused carpels.
  
 +
If the styles are fused at the base but free at the top, the free portions are called "style branches" or "stylodia" (Troll), or "stigma branches" if it is only the stigma portion that is free.
  
−
'''ear lateral meristem (PO:0009110)'''
+
'''stigma:''' Raven defines this as a part of a carpel. Esau is ambiguous about how to treat stigma in syncarpous gynoecium. Weberling refers to a single stigma for fused carpels, but also to multiple stigmas, if the carpels are fused at the base and style, but then free at the tips, where the stigmas are. Also refers to stigma lobes (e.g., a tulip, with three fused carpels, has a single stigma, with three lobes. Seem like we have to treat stigma the same as ovary and style.
  
−
'''current def.:''' The meristem that gives rise to the lateral structures of a maize ear.
+
'''anther and filament'''
  
−
This should be called '''ear inflorescence branch meristem''', and be a subtype of inflorescence branch meristem (PO:0009105). Will need to add XP definitions to the different types of meristems so that they don't have dual parentage (e.g., ear inflorescence meristem XP of is_a inflorescence meristem and part_of ear inflorescence).
+
Weberling: Although filaments are often fused, they are still referred to as individual filaments (e.g., the corona of Narcissus consists of fused filaments (not a single filament), with the anthers inserted on the inner surface). Anthers may also fuse, but it is less common. He uses the term "synanther" of a single structure made of fused anthers (e.g., Gesneriaceae, see this [http://www.flickr.com/photos/fostert/5236399328/ cool picture]).
  
−
'''proposed def.:''' An inflorescence branch meristem that gives rise to the branches of an ear inflorescence.
+
It seems like it would be better to keep anther and filament as part of stamen, since that is the more commmon state. We can use special terminology for when they are fused (such as corona and synather).
  
−
==conductive and related cell types==
+
==Cacti terms:==
−
===Current parent: axial cell===
+
'''spinule:''' word for when the spines are stipules – synonym of stipule spine
−
'''Existing structure:'''
 
  
−
axial cell (PO:0000081)
+
In Beentje, spinule is defined as a small spine.
  
−
>sieve tube member (PO:0000289, alt: PO:0000286)
+
Add "spinule" as narrow synonym for stipule spine and as related synonym for other kinds of spines.
  
−
>phloem fiber (PO:0004519)
+
===[https://sourceforge.net/tracker/?func=detail&aid=3439006&group_id=76834&atid=835555 cladode and phylloclade]===
 +
From Beentje:
  
−
>xylem element (PO:0000273)
+
cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf
  
−
>>tracheary element (PO:0000273)
+
phylloclade: portion of stem or branch (several nodes and internodes) flattened and expanded to serve the functions of a leaf.
  
−
>>>tracheid (PO:0000301)
+
FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
  
−
>>>vessel member (PO:0002003)
+
proposed definition:
  
−
>>xylem fiber (PO:0000274)
+
cladode: A shoot axis that is flattened and expanded.
  
−
>>>fiber tracheid (PO:0000355)
+
comment: Has an increased surface area for photosynthesis and may function similar to a leaf in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes.
  
−
>>>libriform fiber (PO:0004520)
+
synonyms: phylloclade, cladophyll
  
−
>>>septate fiber (PO:0004521)
+
Dennis said: A shoot axis that is flattened. expanded is redundant. What about cholla?
 +
This does not work. The comment also does not work. Similarily the
 +
synonyms are not so much synonyms as they are subsets.
  
 +
''I don't know what the problem is with Cholla. As far as I know, it does not have cladodes or phylloclades, because the axes are round.''
  
−
'''axial cell (PO:0000081):''' A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208]
+
Recent interesting paper on cladodes in Asparagus:  
  
−
Comment: These cells make up the axial system, also known as vertical or longitudinal system.
+
Nakayama,H., Yamaguchi,T. and Tsukaya,H. (2012) Acquisition and Diversification of Cladodes: Leaf-Like Organs in the Genus Asparagus. [http://www.plantcell.org/content/early/2012/03/12/tpc.111.092924.abstract The Plant Cell Online, 24, 929 –940].
  
−
The term axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).
+
PMID:22415273
  
−
Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system.
+
In Asparagus, some cladodes have re-evolved a rounded shape. Are they still cladodes, or just shoot axes again at that point (given that the PO is not based on homology)?
  
−
See [[Items for future meetings#other wood terms]], below.
+
===rib===
 +
Should also add 'rib' for cacti and other plants.
  
−
===New proposed hierarchy (children of plant cell):===
+
Definition:
  
−
plant cell
+
-caryopsis new child of fruit
  
−
>sieve element (new term)
+
-adventitious root nodule
 +
==Make two sub-types of tapetum ==
 +
Based on the discussion on the PO conf call 4-9-13, we need to add the two types of tapetum(s). Added as a comment on tapetum for now.
  
−
>>sieve tube member (syn.: sieve tube element)
+
See tracker at: [https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3298006&group_id=76834 tapetum types]
  
−
>>sieve cell (new term)
+
Comment from DWS: there are two types of tapetum: ameboid and secretory/glandular:
  
−
>tracheary element
+
Need to determine if it is more appropriate to put them as child of tapetum or anther wall tapetum. 
  
−
>>tracheid
+
See references in the literature to: Sporne KR (1973) A Note on the Evolutionary Status of Tapetal Types in Dicotyledons. New Phytologist 72: 1173–1174
  
−
>>vessel member
+
[http://onlinelibrary.wiley.com.ezproxy.proxy.library.oregonstate.edu/doi/10.1111/j.1469-8137.1973.tb02093.x/abstract link]
  
−
>ground tissue cell (PO:0025030)
+
[http://books.google.com/books?id=xBR5KMLYGkUC&pg=PA8&lpg=PA8&dq=glandular+tapetum&source=bl&ots=P8Dfiew3_r&sig=0-Nr93OoExcRcqFFRTGnhKKMQ4A&hl=en&sa=X&ei=CUxkUaucFjriwLEqICoBA&ved=0CGAQ6AEwCA%23v=onepage&q=glandular%20tapetum&f=false#v=snippet&q=glandular%20tapetum&f=false link to book]
  
−
>>sclerenchyma cell (PO:0000077)
+
[http://ir.library.oregonstate.edu/xmlui/handle/1957/9976 link to OSU Thesis]
  
−
>>>sclerid (new term)
 
  
−
>>>fiber cell (new term)
+
==Organizing the types of plant cells ==
  
−
>>>>phloem fiber cell
+
New term added: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/586/ native plant cell (PO:0025606)] and moved all the non cultured types of cells there, but it really needs some organization.
  
−
>>>>xylem fiber cell
+
In CL, they are organized by type: 
 +
* absorptive cell CL:0000212 A cell that takes up and metabolizes substances.
  
−
>>>>other kinds of fiber cells?
+
* ciliated cell ID: CL:0000064 A cell that has a filiform extrusion of the cell surface.
  
−
===New definitions - sieve elements===
+
* barrier cell ID: CL:0000215 A cell whose primary function is to prevent the transport of stuff across compartments.
−
Definitions from Esau's Anatomy of Seed Plants
 
  
−
'''sieve element (new term)'''
+
* defensive cell  CL:0000473  A cell whose primary function is to protect the organism.
  
−
From Esau (glossary): The cell in the phloem tissue concerned mainly with longitudinal conduction of food materials. Classified into sieve cell and sieve tube member.
+
* diploid cell ID: CL:0000415 A cell whose nucleus has two haploid genomes. xref_analog FMA:72300
  
−
Also from Esau (in text): Their principal morphological characteristics are sieve areas (modified pits) in their walls and the absence of nuclei in mature protoplasts.
+
* haploid cell ID: CL:0000413 A cell whose nucleus contains a single haploid genome.
  
−
'''proposed def.:''' A plant cell that is part of a portion of phloem tissue, has sieve areas (modified pits) in its walls, and lacks a nucleus in its mature protoplast.
+
* gamete ID: CL:0000300 A mature sexual reproductive cell having a single set of unpaired chromosomes.
  
−
Comment: Sieve cells function mainly in longitudinal conduction of organic solutes. Classified into sieve cells and sieve tube members based on the presence of sieve plates and specialization of sieve areas in different parts of the cell. Develops from either a cambial initial or a cell of the procambium.
+
* polyploid cell ID: CL:0000412 A cell whose nucleus, or nuclei, each contain more than two haploid genomes.
  
−
part_of phloem, participates_in sporophyte stage
+
* secretory cell ID: CL:0000151 A cell that specializes in controlled release of one or more substances.
  
 +
* transporting cell ID: CL:0000627 A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances.  xref_definition TAIR:sr
  
−
'''sieve cell (new term)'''
+
* supportive cell ID: CL:0000630 A cell whose primary function is to support other cell types.
  
−
proposed def.: A sieve element in which the sieve areas are not aggregated into sieve plates.
+
* somatic cell ID: CL:0002371 A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
  
−
Comment: Sieve areas in sieve cells generally have narrow pores and thin connecting strands, and they are not highly specialized, but instead are fairly uniform throughout the cell wall. Typical of gymnosperms and non-seed vascular plants. Differ from sieve tube members, which have sieve plates and more pronounced specialization of sieve areas.
+
* stem cell CL:0000034 A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
  
 +
* storage cell ID: CL:0000629 A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose.
  
−
'''sieve tube member (PO:0000289)'''
+
* stuff accumulating cell ID: CL:0000325 A cell that is specialised to accumulate a particular substance(s).
  
−
'''current def.:''' One of the series of cells that make up a sieve tube; it shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores).
+
=Revisions to Plant Structure Development Stages:=
 +
''POC 9-10-13: Add comment on how every stage can end in accidental death. Also mention something death being the canonical end point''
  
−
comment: Also sieve tube element and the obsolete sieve tube segment. Occurs in the sporophytic phase of a plant life cycle.
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/ Stages of Plant Embryo Development]==
  
 +
Currently: in Version #20, Aug 2013:
  
−
'''proposed def.:''' A sieve element that is part of a sieve tube and has sieve areas aggregated into sieve plates.
+
[[File:Plant Embryo Dev Stages.png]]
  
−
Comment: Sieve elements have sieve areas that are specialized into those with wide pores in sieve plates and those with with narrow pores in lateral sieve areas. Sieve tube members may have inclined end walls with compound or simple sieve plates. Typical of angiosperms. Differ from sieve cells, which have less pronounced specialization of sieve areas and no sieve plates.
+
Note: Not sure where the coleoptilar stage (PO:0001094) fits in- it has no letter code and apparently never has (at least in the last 4 years). The A zygotic stage term was removed sometime in 2011. Currently the heirarchy looks quite odd as starts with "B- proembryo stage"
  
−
syn.: sieve tube element, sieve tube segment
+
''-Removed the letters in the names and added preceded_by to order the stages. made coleoptilar stage (PO:0001094) a subclass of  bilateral stage (PO:0004507). ''
  
−
part_of sieve tube (new term)
+
===Revisions June-July 2014:===
 +
[[File:Screen Shot 2014-07-14 at 2.33.52 PM.png]]
  
 +
* '''[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=1#fde8 plant embryo development stage (PO:0007631)]''': A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the '''first cell division of a plant zygote (PO:0000423)''' and one of the following:
 +
** the beginning of the seed germination stage (PO:0007057) in seed plants,
 +
** the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
 +
** formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes,
  
−
'''See below for companion cells and other parenchyma cells found in vascular tissue.'''
+
 +
''An issue with the current definition is that it excludes the cotyledonary and true leaf formation stages, no?  Also, the seed germination stage (PO:0007057) is defined as starting with seed imbibition. ''
  
−
====New term for sieve tube====
 
  
−
'''sieve tube, proposed definition:''' A portion of phloem tissue that has as parts a series of sieve tube members arranged end to end and interconnected through sieve plates.
 
  
−
====New terms for GO====
 
−
These subcellular components have been requested from GO.
 
  
−
'''sieve area:''' A cell wall part that is a pit-like area in a plant-type cell wall of a sieve element and has as parts pores lined with callose and occupied by strands of protoplasmic material that interconnect the protoplasts of contiguous sieve elements.
+
** Comment: Succeeds a plant zygote stage (PO:0001097). The plant embryo development stage generally starts after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. No plant species undergoes all of the sub-stages listed here.
  
−
is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505); part_of sieve element (PO:xxxx) - may have to go in comment
+
===Sub-classes:===
  
 +
====plant proembryo stage (PO:0001180)]====
 +
'''[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=2#859b plant proembryo stage (PO:0001180)]''': A plant embryo development stage (PO:0007631) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and the onset of the plant globular embryo stage (PO:0001185).
 +
*comment: The plant proembryo stage occurs prior to the differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)).
  
−
'''sieve plate:''' A cell wall part that is the part of a wall of a sieve tube member that bears one or more highly specialized sieve areas.
 
  
−
comment: Typical of angiosperms.
+
-
  
−
is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505), has_part sieve area (GO:xxxx); part_of sieve tube member (PO:xxxx).
+
====plant embryo globular stage (PO:0001185)====
 +
''' [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=2#58b6 plant embryo globular stage (PO:0001185)]''': A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry.
 +
** comment: During the plant globular embryo stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.
  
−
Could add the relation callose deposition in phloem sieve plate (GO:0080165) inheres_in sieve plate.
+
Comments from SF-RW:
 +
''"We need a way to distinguish the end of the proembryo and the beginning of this stage. I think the end can be distinguished by bilaterality. I will have to do some research to see if there are differences in when a proembryo stage ends across land plants."''
  
 +
''"According to Howell 1998, "Proembryo is the term given to describe the embryo up to the stage when the protoderm can be recognized, which is usually the globular stage." (reference?)''
  
−
'''compound sieve plate:''' A sieve plate that has as parts several specialized sieve areas in either a scalariform or reticulate arrangement.
+
''"Of course, the problem with this is that we define the protoderm as arising from an apical meristem, and that is not the case in the embryo. Seems like some authors refer to it as an epidermis and some as a protoderm at this stage. I am not an expert in this, but I think I feel more comfortable with calling it a protoderm rather than a fully developed epidermis. In that case, I suggest modifying the definition of protoderm, which I will post on isssue 125."''
  
−
comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.  
+
''presumably, this is referring to: (https://sourceforge.net/p/obo/plant-ontology-po-term-requests/125/)''
  
−
is_a sieve plate
 
  
 +
''proposed definition RW:''
 +
* '''plant embryo globular stage (PO:0001185)''': A plant embryo development stage (PO:0007631) that occurs during the interval between when a protoderm (PO:0006210) is first recognizable in a plant embryo (PO:0009009) and the onset of a plant embryo bilateral stage (PO:0004507).
  
−
'''simple sieve plate:''' A sieve plate that has as part a single specialized sieve area.
+
New comment: During the plant embryo globular stage, a plant embryo proper (PO:0000001) increases in diameter through cell division but retains radial symmetry, and differentiation of the three main tissue systems (vascular system (PO:0000034), epidermis (PO:0005679), and the portion of ground tissue (PO:0025059)) begins. During a plant embryo bilateral stage, the embryo begins to develop bilateral symmetry. Preceded by a plant proembryo stage (PO:0001180).
  
−
comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.
+
''Propose re-revised def'n LC'':  
 +
* '''plant embryo globular stage (PO:0001185)''': A plant embryo development stage (PO:0007631) that occurs during the interval between when a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry, with the concomitant formation of a protoderm (PO:0006210), and the onset of a plant embryo bilateral stage (PO:0004507).
  
−
===New definitions - tracheary elements===
+
comment: During the plant globular embryo stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.
  
−
'''xylem element (PO:0000273):''' A cell making up xylem tissue.
+
I would avoid describing the plant embryo bilateral stage here as it is confusing to the user. Could also mention the development of the embryo hypophysis (PO:0020109).  
  
−
Currently, this is parent of tracheary element and xylem fiber. I suggest we '''obsolete''' it and make xylem fiber cell a child of fiber cell. Xylem element could be a broad synonym of tracheary element and xylem fiber.
 
  
 +
[http://www.sciencemag.org/content/266/5185/605.abstract?sid=b709ed1b-8241-480e-82d2-17a5d62dfbce Goldberg et al, 1994 Science]:
 +
""Two critical events must occur after the embryo proper forms: (i) regions along the longitudinal apical-basal axis must differentiate from each other and generate embryonic organ systems, and (ii) the three primordial tissue layers of the embryo need to be specified. Both of these events take place during the globular-heart transition phase (Fig. 2 and Table 1). The embryo proper has a spherical shape during the proembryo and globular stages (Fig. 2). The first visible cell differentiation events occur at the 16-cell stage when the protoderm, or outer cell layer of the embryo proper, is produced and the hypophysis forms at the top of the suspensor (Fig. 2). Subsequent cell differentiation events within the embryo proper result in the production of an inner procambium tissue layer and a middle layer of ground meristem cells (Fig. 2)."
  
−
'''tracheary element (PO:0000290)'''
 
  
−
current def.: General term for any water conducting cell, tracheid or vessel member.
 
  
−
Currently is part_of primary xylem and part_of secondary xylem.
+
''Revised def'n LC:''
  
−
proposed def.: A plant cell that has a lignified cell wall with secondary thickening and bordered pits and is dead at maturity.
+
'''plant embryo globular stage (PO:0001185)''': A plant embryo development stage (PO:0007631) that occurs during the interval between when a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry (with the concomitant formation of a protoderm (PO:0006210)), and the onset of a plant embryo bilateral stage (PO:0004507).
  
−
comment: More or less elongated and with pits of various types in the cell wall. Tracheary elements function in the conduction of water and dissolved substances such as mineral nutrients from the roots to the shoot system. Tracheary elements can be distinguished from fiber cells by the presence of bordered pits, although there are intermediate forms called fiber tracheids.
 
  
−
participates_in sporophyte stage, part_of xylem, disjoint from hydroid
+
--
  
 +
====plant embryo bilateral stage (PO:0004507)====
 +
'''[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=2#1329 plant embryo bilateral stage (PO:0004507)]''':  was: Change from radial to bilateral symmetry takes place during this embryonic stage.
  
−
'''tracheid (PO:0000301)'''
+
revised def'n: A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) develops bilateral symmetry.
  
−
current def.: In the xylem, a dead elongated water-conducting cell in which at least the middle lamella of the end walls remains intact.
 
  
−
proposed def.: A tracheary element that has no perforations.
+
''RW: New proposed definition:''
  
−
comment: May have any of the kinds of secondary wall thickenings found in tracheary elements. The area of contact between two tracheids has only bordered pits, whereas in vessel members it has perforations organized into perforation plates.
+
'''* plant embryo bilateral stage (PO:0004507)''': A plant embryo development stage (PO:0007631) that occurs during the interval between the transition from radial to bilateral symmetry in a plant embryo proper (PO:0000001) and the onset of a plant embryo expanding cotyledon stage (PO:0001078).
  
 +
new comment: During a plant embryo expanding cotyledon stage, the embryo axis (PO:0019018) and embryo cotyledons (PO:0025470) begin to elongate. A plant embryo bilateral stage contains the stage commonly known as the heart stage. Preceded by a plant embryo globular stage (PO:0001185).
  
−
'''vessel member (PO:0002003)'''
+
Ref: [http://www.ncbi.nlm.nih.gov/pubmed/24784759 PMID:24784759]
  
−
current def.: One of the cellular components of a vessel, a dead cell with the wall between adjacent members being variously perforated and the walls that persist variously thickened.
 
  
−
proposed def.: A trachary element that is part of a vessel and has as parts perforation plates.
+
--
  
−
Comment: The cell wall of a vessel member has openings called perforations, which are organized into perforation plates (GO:xxxx). These are usually on the end walls of a cell, but may also be on the side walls. A perforation plate may be simple, with one perforation, or multiperforate, with more than one perforation.
 
  
−
syn.: vessel element, vessel segment
 
  
−
part_of vessel (new term)
 
  
  
−
'''vessel (new term)'''
 
  
−
proposed def.: A portion of vascular tissue that has as parts a tube-like series of vessel members, the common walls of which have perforations.
 
  
 +
--
  
−
'''perforation plate''' (for GO)
+
===Suggested revisions from Dora Szakonyi (from 2012-06-27):===
 +
* See Open SF tracker: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/488/ #488 embryo development terms]
 +
* At the moment '''B proembryo stage_PO:0001180''' is a synonym for both 'eight-celled stage in Arabidopsis' and 'two-celled stage in Arabidopsis'. Maybe it would be good to introduce as child terms separately:
  
−
proposed def.: A cell wall part that is the part of a wall of a vessel member that bears one or more openings (perforations).
+
'''* B proembryo stage_PO:0001180 (= preglobular stage)'''
 +
# two-celled stage in Arabidopsis
 +
# four-celled stage in Arabidopsis (= quadrant stage)
 +
# eight-celled stage in Arabidopsis (= octant stage)
  
−
comment: May be simple, with one perforation, or multiperforate, with more than one perforation. Perforation plates are usually on the end walls of a cell, but may also be on the side walls.
+
'''* Similarly, for '''C globular stage_PO:0001185''' new child terms:'''
 +
# dermatogen stage in Arabidopsis (=16-cell stage)
 +
# early-globular stage in Arabidopsis (32-cell stage)
 +
# mid-globular stage in Arabidopsis
 +
# late-globular stage in Arabidopsis
  
−
===New definitions - ground tissue cells===
+
'''* For D bilateral stage_PO:0004507'''
 +
# Transition stage in Arabidopsis (=triangular stage)
 +
# early-heart stage in Arabidopsis
 +
# mid-heart stage in Arabidopsis
 +
# late-heart stage in Arabidopsis
  
−
'''sclerenchyma cell (PO:0000077)'''
+
'''* E expanded cotyledon stage_PO:0001078'''
 +
Linear cotyledon stage embryo
 +
# early-torpedo stage in Arabidopsis
 +
# mid-torpedo stage in Arabidopsis
 +
# late-torpedo stage in Arabidopsis
 +
# Bent cotyledon stage (curled cotyledon stage/walking stick stage)
  
−
current def.: Usually dead cell variable in form and size, with more or less thick, often lignified, secondary walls.
+
'''* F mature embryo stage_PO:0001081'''
  
−
proposed def.: A ground tissue cell with thickened secondary cell walls that are often lignified.
 
  
−
comment: May or may not be devoid of protoplast at maturity. Not always easy to distinguish from xylem tissue or sclerified parenchyma cells.
+
Older trackers:  
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/ #400 plant embryo stage]
  
−
Currently, sclerenchyma cell part_of sclerenchyma, but this is not always true. There can be isolated sclerenchyma cells.
+
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/426/ #426 spore and embryo dormant stages]
  
 +
References:
 +
* [https://www.mcdb.ucla.edu/Research/Goldberg/research/Pdf/Science-1994-Goldberg-605-14.pdf Goldberg et al, 1994 Science]
 +
* [http://masish.uab.cat/masish/images/maizeseedanatomy2.pdf maize embryo development]
  
−
'''sclerid (new term)'''
+
=Other "To do" items:=
 +
* Next: start working on the fruit ripening stages, leaf and and tuber development stages- see below
 +
* Complete edits on prothallial cell and prothallium
 +
* Post list of phloem terms to tracker- what needs to be done on them?
 +
* follow up with French fern folks about terms for ferns - email inquiry, terms on tracker
 +
* reopen gametophyte and sporophyte?
 +
* Resolve the question about axis vs stem
 +
* Open tracker for new term for caryopsis, other types of fruit
 +
* look at spikelet rachilla (PO:0009080): The axis of the spikelet, above the glumes. is_a inflorescence branch (PO:0025111).  needs to be revised. tracker?
 +
* [https://sourceforge.net/tracker/index.php?func=detail&aid=3405173&group_id=76834&atid=835555 spikelet] needs to be revised
 +
* ovary wall should not be a cardinal organ part as ovary is not an organ ''See [[Items_for_future_meetings#ovary_and_the_like]] below.''
 +
* pappus element should not be a COP, as a pappus is not an organ- collective organ part structure. ''Each pappus element is a part of some organ (although there is some debate about which organ it is part of), thus pappus element is a cardinal organ part. The pappus is a collection of pappus elements, and therefor a collective organ part structure. I think the classification is correct.''
 +
* egg apparatus- should not be a COP, as it part_of embryo sac which is_a megagametophyte which is_a whole plant ''This was classified back when we were looser with putting things under COP. Need to propose an alternative classification. Maybe a portion of plant tissue?''
 +
* there are a number of parts of fruit such as the fruit septum (PO:0025268), fruit locule, fruit valve that should have dual parentage- e.g. fruit septum is_a septum (is_a col. organ part structure) and should also be is_a cardinal part of a multi-tissue plant structure.
 +
* Need to revisit the AISO annotations of segmented images, as some of the protoxylem terms are not in the live version yet (will be in Release #20).
 +
* Need to work on the development of the gametophytes in moss [http://www.plantphysiol.org/content/162/3/1406.full Moss Physcomitrella patens Reproductive Organ Development, Plant Phys, 2013]
 +
* Add PO:id for tapetum (PO:0025313) to comment on tapetum cell (PO:0025543)
 +
* need to fix: paraclade cortex PO:0004721: A portion of ground tissue that is part of a cortex and part of a paraclade. - ''change to 'primary inflorescence branch cortex'; add PO:Ids''
 +
* Add preceded_by to the sub-classes of floral organ formation stage (PO:0025585): 
 +
* Need to fix: spikelet rachilla: (PO:0009080): The axis of the spikelet, above the glumes. [source: POC:curators] ''- Should be an inflorescence branch (primary?), add PO:Ids''
 +
* look at caruncle (PO:0020060) again- came up in the contest of the arillode and arilloid.
 +
* Add a comment on the top level term about how all PSDS's may be terminated before reaching senescence stage.
 +
* should we add a costa has part hydrome and leptome, they are not always there?
  
−
proposed def.: A sclerenchyma cell that has thick, lignified secondary walls with many pits.
+
* fix comment on receptacle- strawberry is an accessory fruit, post on tracker
  
−
comment: Usually not very elongated.
+
* need to revisit the portion of meristem tissue definition- about 2 dozen direct is_a children, many of which are actually determinate tissues such as the phyllome anlagen (PO:0025430) and child terms, the primordium, etc
  
−
====parenchyma cells in vascular tissue====
+
* Need to revisit [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/145/  shoot node (PO:0005004)]: A cardinal organ part of a shoot axis where one or more spikelet, flower, floret, branch, bud, or leaf may arise.  ''Refer to the POC call 10-1-13 for more details.''
  
−
'''companion cell (PO:0000071)'''
+
* Need to revise 'root epidermis (PO:0006036)' to match the shoot system epidermis PO:0006035 (see [[POC_Conf._Call_10-29-13]])
  
−
'''current definition:''' A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member.  
+
* Consider getting rid of apical meristem (PO:0020144)- it forces dual parentage on the two child terms- shoot apical meristem (PO:0020148) and root apical meristem (PO:0020147) and forms a loop/cycle.
  
−
'''proposed definition:''' A parenchyma cell that is adjacent to a sieve-tube member and arises from the same mother cell as the sieve-tube member.
 
  
−
comment: Found in angiosperms. Compare to albuminous cells (PO:xxxx), which are found in gymnosperms.
 
  
−
Currently part_of primary phloem '''and''' part_of secondary phloem, which can't be true. Should change to part_of phloem.
 
  
−
Suggest that we add relation companion cell adjacent_to sieve tube element.
 
  
 +
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/499/ whole plant flowering stage PO:0007016]==
 +
* Now that we have revived the flowering stages, we need to revisit the whole plant flowering stages:
  
−
'''albuminous cell (new term)'''
+
whole plant flowering stage (PO:0007016): A sporophyte reproductive stage (PO:0007130) during which a flower (PO:0009046) on a whole plant (PO:0000003) is open.
  
−
'''proposed def.:''' A parenchyma cell that is morphologically and physiologically associated with a sieve cell but does is not derived from the same initial cell as the sieve cell.
+
''This is incorrect as in many plants, pollination occurs before the flowers open, especially self-pollinated plants''
  
−
comment: May be found in the rays and sometimes the axial system of gymnosperms. Compare to companion cells, which are found in angiosperms.
+
* child terms need to be revised and the synonyms need to be reviewed, compare synonyms and stages
 +
** PO:0007026 : FL.00 first flower(s) open stage [24,868]
 +
** PO:0007034 : FL.01 1/4 of flowers open stage
 +
** PO:0007053 : FL.02 1/2 of flowers open stage [0]
 +
** PO:0007052 : FL.03 3/4 of flowers open stage [0]
 +
** PO:0007024 : FL.04 end of flowering stage [2]
  
−
is_a parenchyma cell, part_of phloem, adjacent_to sieve cell.
+
''Why are there ~25,000 associations on the first one and none on the rest? They look like they are all from Zea Mays, and 1 from SGN. ''
  
  
−
Should we have a term for phloem parenchyma cell? Could be parent of companion cell and albuminous cell.
+
==fruit development stages (PO:0001002)==
 +
* See [https://docs.google.com/spreadsheet/ccc?key=0AvF6MNosp3qTdDZEMzBVdXJWZjVubkJNVlBtSmQ2WFE&usp=sharing Google Doc] for revisions in progress.
  
−
====fiber cells====
+
* To avoid confusion, the whole plant fruit development stages (PO:0025500) were renamed in [[Release_19]] to make it clear that they apply to whole plants.
−
'''fiber cell (new term)'''
 
  
−
proposed def.: An elongated, tapering schlerenchyma cell with a more or less thick secondary cell wall.
+
* The plant phenotype pilot project needs terms for grain (fruit) development stages such as milk stage (as synonym for more general term) and mature or dry stage.  
  
−
comment: May or may not have lignin in the secondary wall or a living protoplast at maturity. It may be difficult to distinguish fiber cells from xylem cells.
+
* We currently have terms for two sub-classes:
 +
**fruit formation stage PO:0025501  [145]
 +
*** PO:0025503 : fruit initiation stage [0]
 +
*** PO:0025505 : fruit size 10 to 30% stage [0]
 +
*** PO:0025506 : fruit size 30 to 50% stage [0]
 +
*** PO:0025507 : fruit size 50 to 70% stage [0]
 +
*** PO:0025508 : fruit size 70% to final size stage [0]
 +
*** PO:0025504 : fruit size up to 10% stage [0]
 +
** PO:0025502 : fruit ripening stage [118]
  
 +
====fruit ripening stage PO:0025502 and sub-classes====
 +
New terms are needed to describe the stages of ripening for individual fruits.  Have a revised parent term; need the sub-classes.
  
−
'''phloem fiber cell (PO:0004519)''' (was called phloem fiber)
+
[https://sourceforge.net/tracker/index.php?func=detail&aid=3577380&group_id=76834&atid=835555 fruit ripening stage]: A fruit development stage (PO:0001002) during which a single fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).
  
−
current def.: A fiber in phloem.
+
Comment: Succeeds a fruit formation stage (PO:0025501). This stage is to be used for an individual fruit. Fruit ripening (GO:0009835) is defined as: an aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal. For the development stage of a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).
  
−
proposed def.: A fiber cell that is part of a portion of phloem tissue.
 
  
 +
[http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=GO&termId=GO%3A0009835&termName=fruit%20ripening fruit ripening] (GO:0009835): An aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal.
  
−
'''xylem fiber cell (PO:0000274)''' (was called xylem fiber)
+
related synonyms: fruit maturation; fruit senescence
  
−
current def.: A fiber in xylem.
+
==PO:0001170 : seed development stage [33916]==
 +
* PO:0004506 : developing seed stage [10]
 +
* PO:0001040 : dry seed stage [19]
 +
* PO:0007633 : endosperm development stage [33495]
 +
* PO:0004505 : fertilized ovule stage [4]
 +
* PO:0025374 : seed dormant stage [23]
 +
* PO:0007632 : seed maturation stage [12]
  
−
proposed def.: A fiber cell that is part of a portion of xylem tissue.
+
==plant organ development stage (PO:0025339) and child terms:==
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/548/ phyllome development stage (PO:0025579)]: A plant organ development stage (PO:0025339) that has a primary participant a phyllome (PO:0025023) (Created in Release Version #19 )
  
−
comment:  
+
* moved leaf development (PO:0001050) to be subclass of phyllome development stage, will be adding flower bract development (PO:new) see below.
  
 +
[[File: phyllome_snap_shot.jpg]]
  
−
'''libriform fiber (PO:0004520)'''
+
Comment: Includes stages for the initiation, expansion, and senescence of a phyllome such as a leaf, lemma, or stamen.
  
−
current def.: A xylem fiber commonly with thick walls and simple pits.
+
==reproductive shoot system development stage (PO:0025530)==
 +
* Is_a: collective plant organ structure development stage (PO:0025338)
  
−
proposed def.: A xylem fiber cell with simple pits.
+
* We need to build a hierarchy for the development of '''conifer cones-''' as they are also reproductive shoot systems
  
−
Comment: Libriform fibers have unbordered pits while fiber tracheids have bordered pits. Many intermediate forms exists and are generally classified as fiber tracheids. If both libriform fibers and fiber tracheids are present, the libriform fibers usually have thicker walls. Libriform fibers have a slit-like aperature toward the cell lumen, but no pit cavity.  
+
** A conifer cone is a '''strobilus (PO:0025083):'''  A reproductive shoot system consisting of a number of modified leaves (sporophylls) or ovule-bearing scales grouped terminally on a stem. [source: ISBN:0716710072, POC:curators]
 +
*** Comment: May be simple or compound. Found in lycophytes such as Selaginella and Lycopodium, sphenophytes such as Equisetum, gymnosperms such as cycad, conifers, gnetophytes and the pollen producing structures of Gingko. The term cone is often used for strobili that are woody. Flowers are sometimes considered bisexual strobili. Some flowering plants such as Alnus have inflorescences called catkins that resemble strobili, but are not.
  
 +
* moss reproductive structures: these would both be children of plant organ development, as moss lacks a shoot system.
 +
** multicellular plant gametangium (PO:0025124):- antheridium (PO:0025125) and archegonium (PO:0025126)- produce the gametes
 +
** sporangium (PO:0025094): A plant organ in which spores are produced.
  
−
'''fiber tracheid (PO:0000355)'''
 
  
−
current def.: A fiber-like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures.
+
''Need to look at the fern sporangia- that is the reproductive structure for those plants''
  
−
Should this be is_a xylem fiber or is_a tracheid? Esau's definition says it is a tracheid, but her treatment it the book is as a fiber.
 
  
−
proposed definition: A xylem fiber cell with bordered pits with pit cavities.
 
  
−
comment: If both libriform fibers and fiber tracheids are present, the libriform fibers usually have thicker walls. Fiber tracheids have bordered pits with smaller pit cavities than the vessels or tracheids of the same wood and a distinct pit cavity leading from the pit cavity to the cell lumen through the thick cell wall.
+
* This would parallel the two existing sub-classes:
  
 +
==inflorescence development stage (PO:0021004)and sub-classes==
 +
* Currently linked to  tracker for: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/517/ shoot system development stages and child terms]
  
−
'''septate fiber (PO:0004521)'''
+
* Currently this has two sub-classes:
 +
 +
** PO:0021004 : inflorescence initiation stage [0]
 +
** PO:0007037 : inflorescence bifurcation stage [0]
  
−
current def.: A fiber with thin transverse walls (septa), which are formed after the cell develops a secondary wall thickening.
+
* Inflorescence development stage (PO:0001083):A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).
 +
** inflorescence initiation stage (PO:0021004): Stage of inflorescence development marked by the formation of the inflorescence meristem on a vegetative branch. [source: POC:Felipe_Zapata]
 +
** inflorescence bifurcation stage ( PO:0007037): Stage of inflorescence development marked by the formation of two, often equal-sized, inflorescence meristems from one inflorescence meristem. [source: POC:curators]
  
−
Septate fibers can be found in both the xylem and the phloem. PO:0004521 is_a xylem fiber, but both tracheid-type and libriform-type xylem fibers can be septate. There are no annotations on this term, so I suggest we obsolete it, and replace it with two new terms: septate fiber tracheid and septate libriform fiber. Could also add septate phloem fiber, is_a phloem fiber.
+
These need to be revised and additional stages need to be developed.
  
−
'''proposed definition, septate fiber tracheid:''' A fiber tracheid that has as parts one or more thin internal partitions or septa.
+
==flower development stage:==
 +
This is mostly done- this reference might be helpful for the legume flowers and have annotations to add.
 +
Floral Development in Legumes: (Plant Physiol, March 2003, Vol. 131, pp. 911-926)
  
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
+
==collective phyllome structure development stage (PO:0025578) and child terms==
  
−
'''proposed definition, septate libriform fiber:''' A libriform fiber that has as parts one or more thin internal partitions or septa.
+
[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/547/ collective phyllome structure development stage (PO:0025578)]: A collective plant organ structure development stage (PO:0025338) that has as primary participant collective phyllome structure (PO:0025023).  
  
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
+
* Made these part_of floral organ differentiation stage (PO:0007600), need to work on the definitions....
  
−
'''proposed definition, septate phloem fiber:''' A phloem fiber cell that has as parts one or more thin internal partitions or septa.
+
** '''androecium development stage (PO:0007605):''' A collective phyllome structure development stage (PO:0025578) that has as a primary participant an androecium (PO:0009061).  
  
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
+
** '''calyx development stage (PO:0007603):'''A collective phyllome structure development stage (PO:0025578) that has as a primary participant a calyx (PO:0009060).
  
 +
** '''corolla development stage (PO:0007604):'''A collective phyllome structure development stage (PO:0025578) that has as a primary participant a corolla (PO:0009059).
  
−
====other kinds of fiber cells?====
+
** '''gynoecium development stage (PO:0007606):''' A collective phyllome structure development stage (PO:0025578) that has a primary participant a gynoecium (PO:0009062).
  
−
'''gelatinous fiber:''' A xylem fiber cell in which the inner-most layer of the secondary wall contains abundant alpha-cellulose and is poor in lignin.
+
[[File: collective_phyllome_snap_shot.jpg]]
  
−
comment: Commonly found in reaction wood in dicots. The inner layer of the cell wall, or G-layer, can absorb much water and swell and is relatively porous and less compact than the outer layers of the cell wall.
+
===New term flower bract development stage (new po:id)===
 +
 +
flower bract development stage (new po:id):  
  
−
ref: Fahn
+
- will be parent to lemma development stage and palea development stage
  
−
synonym: mucilaginous fiber
+
* lemma development stage (PO:0001047): A phyllome development stage (PO:0025579) that has as a primary participant a lemma (PO:0009037).
 +
** PO:0001055 : lemma primordia visible stage [1]
 +
** PO:0001056 : lemma differentiation and expansion stage [0]
 +
** PO:0001057 : fully expanded lemma stage [0]
 +
  
 +
* palea development stage (PO:0001048): A phyllome development stage (PO:0025579) that has as a primary participant a palea (PO:0009038).
 +
** PO:0001058 : palea primordia visible stage [1]
 +
** PO:0001070 : palea differentiation and expansion stage [0]
 +
** PO:0001071 : fully expanded palea stage [0]
  
−
'''extraxylary fiber?''' - a fiber cell outside the xylem. Would include phloem fibers, fibers as idioblasts, and fibers in ground tissue.
+
==anther development stage (PO:0001004) and its child terms==
 +
* [https://sourceforge.net/tracker/?func=detail&aid=3613820&group_id=76834&atid=835555 anther development stage (PO:0001004)]: Stages of development of the anther defined by characteristic morphological, cytological, histological or other visible features.
 +
*Is_a androecium development stage (PO:0007605):
  
−
==other wood terms==
+
* In Release #19, we renamed ''anther wall tapetum degeneration initiated stage  (PO:0001032):'' An anther development stage during which degeneration of the anther wall tapetum (PO:0009071) is initiated, as the deposition on the surface of the microspore (PO:0020048) primexine proceeds.  
−
'''Wood''' is a synonym for secondary xylem (PO:0005848) -- see definition above.
 
  
−
'''axial system:''' A portion of plant tissue that has as parts cells derived from the fusiform cambial initials and oriented with their longest diameter parallel to a root or shoot axis.
+
Blackmore S, Wortley AH, Skvarla JJ, Rowley JR (2007) Pollen wall development in flowering plants. New Phytologist 174: 483–498
  
−
comment: Includes portions of secondary xylem tissue and axial wood parenchyma tissue.
+
==[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 tuber growth and development stages]==
 +
This item has been open on SF since 6/2009, How we work these in will depend on restructuring of PSDS
  
−
synonyms: vertical system, longitudinal system
+
We will have to differentiate between the two sub-types of tuber (PO:0025522), as they will have different development:
 +
* tuber (PO:0025522): A plant axis (PO:0025004) that is radially enlarged. [source: POC:curators]
 +
* PO:0004543: shoot axis tuber [6]
 +
* PO:0025476: tuberous root tuber [0]
  
 +
So the main classes could be under: is_a plant axis development stage (PO: new) is_a plant organ development stage (PO:0025339)
  
−
'''ray system:''' A portion of parenchyma tissue that has as parts all of the ray wood parenchyma in a plant structure.
 
  
−
comment: May refer to the ray system of a shoot axis, a root, or an entire plant.
+
From Naama Menda: "I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).
  
−
synonyms: radial system, horizontal system
+
Suggested stages:
−
 
+
* tuber initiation
−
 
+
* tuber growth
−
 
+
* tuber maturation
−
'''wood parenchyma (PO:0004532):'''
 
−
 
 
−
Current def.: Parenchymatous tissue occurring in the wood.
 
−
 
 
−
is_a secondary xylem. Should be is_a parenchyma.
 
−
 
 
−
 
 
−
Proposed def.: A portion of parenchyma tissue that is part of a portion of secondary xylem.
 
−
 
 
−
 
 
−
'''wood parenchyma cell (PO:0004525):'''
 
−
 
 
−
Current def.: Parenchyma cell occurring within secondary xylem.
 
−
 
 
−
Proposed def.:
 
−
 
 
−
 
 
−
'''axial wood parenchyma (PO:0004533):'''
 
−
 
 
−
Current def.: Parenchyma tissue in the axial system of secondary xylem.
 
−
 
−
 
 
−
axial wood parenchyma cell ; PO:0004526 Parenchyma cell in the axial system of secondary xylem.
 
−
plant anatomy
 
−
 
 
−
 
 
−
procumbent wood ray parenchyma cell ; PO:0004529 Ray cell within secondary xylem having its longest axis in radial direction.
 
−
 
 
−
 
 
−
'''ray wood parenchyma (PO:0004534):'''
 
  
−
Current def.: Radially oriented parenchyma tissue in secondary xylem.
+
''Would these be the same for the two different types of tubers? Also need: tuber dormancy''
  
−
Proposed def.: A portion of parenchyma tissue that develops from ray initials and extends radially in the secondary xylem and phloem of a plant axis.
+
* sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
  
−
comment: Occurs in bands or rays of variable width and height.  The term ray system is used to describe all of the rays in a plant structure.
+
* All the SGN annotations refer to potato, which is a subterranean tuber (PO:0004547)
 +
**part_of children:
 +
*** PO:0025070 : subterranean tuber axillary bud meristem
 +
*** PO:0025081 : subterranean tuber axillary shoot (exact synonym: tuber sprout)
 +
*** PO:0025042 : subterranean tuber axillary vegetative bud (narrow synonym: potato eye)
 +
*** PO:0025048 : subterranean tuber epidermis
 +
*** PO:0025045 : subterranean tuber periderm
 +
*** PO:0025038 : subterranean tuber storage parenchyma
  
−
part_of ray system
 
  
 +
===Further info and references:===
 +
[http://www.cals.uidaho.edu/potatoes/potatoproductionsystems/topics/growth&development.pdf Potato Growth & Development]
  
−
'''ray wood parenchyma cell (PO:0004527):'''
+
[http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2005.00141.x/full Tuber on a chip: differential gene expression during potato tuber development]
  
−
Current def.: Parenchyma cell of a ray in secondary xylem.
+
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540956/pdf/plntphys00369-0069.pdf Growth of the Potato Tuber]
  
−
Proposed def.: A parenchyma cell that is part of a portion of ray wood parenchyma.
+
=xylem developmental stages: =
  
 +
See discussions of primary xylem on [http://wiki.plantontology.org/index.php/POC_Conf._Call_6-11-13 POC_Conf._Call_6-11-13]
  
−
upright wood ray parenchyma cell ; PO:0004528 Ray cell in secondary xylem oriented axially (vertically in the axis) with its longest dimension.
+
Existing definitions:
  
 +
'''* secondary xylem development stage (PO:0025427)''': A xylem development stage (PO:0025425) that has as primary participant a portion of secondary xylem (PO:0005848) tissue during the interval between the beginning of a cell division stage of secondary xylem (PO:0025463) and the death of the last living cell in the secondary xylem. [source: POC:wood_curators]
  
 +
*Need:  primary xylem development stage (PO:new): A xylem development stage (PO:0025425) that has as primary participant a primary xylem (PO:0005849) tissue. '' needs to be expanded''
  
−
'''sapwood (PO:0004513):'''
+
=whole plant development stages (PO:0007033)=
 +
* sporophyte vegetative stage (PO:0007134):
 +
child terms need to be revised:
 +
** plant embryo stage (PO:0007631)
 +
** 0 seed germination stage (PO:0007057)
 +
** coleoptile emergence stage (PO:0007045)
 +
** 1 main shoot growth stage (PO:0007112)
 +
** 2 formation of axillary shoot stage (PO:0007073)
 +
** seedling development stage (PO:0007131)
  
−
Current def.: Outer part of the wood of stem or root containing living cells and reserves and in which conduction of water takes place. Generally lighter colored than the heartwood.
+
==whole plant fruit ripening stage (PO:0007010)==
 +
* [https://sourceforge.net/tracker/index.php?func=detail&aid=3565059&group_id=76834&atid=835555 whole plant fruit ripening stage]: A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.  
  
 +
Comment:
 +
Succeeds a whole plant fruit formation stage (PO:0007042). This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit ripening stage (PO:0025502). Although individual fruits are undergoing fruit ripening (GO:0009835), which is a type of senescence, during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An iteroparous species generally will have only one fruit ripening stage in its life, while a semelparous species may have multiple fruit ripening stage in its life. A whole plant fruit ripening stage may be followed by a sporophyte senescent stage, as in case (1) or by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species and species that fruit multiple times during a growing season, a plant may have multiple fruit development stages without entering dormancy or senescence, as in case (3). In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the whole plant fruit formation stage (PO:0007042) has ended. In some plants, fruit may continue to ripen after the whole plant has entered a sporophyte dormant stage or sporophyte senescent stage and left the whole plant fruit ripening stage. Some plants may never enter a whole plant fruit ripening stage, because fruits only begin to ripen after the plant has entered a sporophyte dormant stage or sporophyte senescent stage. Although the use of synonyms like "10-dough stage in sorghum" properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.
  
  
−
early wood ; PO:0004515 The wood formed in first part of a growth ring and characterized by a lower density and larger cells than the late wood.
+
  **Add link to this tracker from the whole plant fruit ripening stage (PO:0007010)**
  
−
heartwood ; PO:0004512 The inner layers of secondary xylem that have largely ceased to function in storage and conduction and in which reserve materials have been removed or converted into heartwood substances; generally darker colored than the functioning sapwood.
+
===See comments from BS from email:===
 +
* On Wed, Sep 18, 2013
  
−
late wood ; PO:0004516 The secondary xylem formed in the later part of a growth ring; denser and composed of smaller cells than the early wood.
+
- A lot of this needs to go, I think:  
  
−
=[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]=
+
- early, middle and late are okay, but then we need to define them non-circularly and if you want to keep whole plant f.r. complete stage' then you have to define it so that it differs from 'late ...'
  
−
All trackers are now closed. Leaving notes about bristle here for when we are ready to describe phenotypes.
+
[[File:WPFRS.png]]
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle]===
+
===Proposed Revisions to sub-classes:===
  
−
(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
+
Comment from RW: The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point.
  
−
''Meeting of RW, MAG and DWS on 8/29/11: we felt this would be better left as a phenotypic descriptor. Should add terms needed to PATO.''
+
need to open tracker for this set:
  
−
''At the POC meeting on 9-27-11, it was decided that bristled stipules should best be handled as a phenotype term. Leaving these notes here for when we start to add phenotypic descriptors.''
+
'''* whole plant beginning of fruit ripening stage (PO:0007036):'''
  
 +
current name and def'n:FR.00 beginning of fruit ripening stage (PO:0007036): The stage at which fruit maturation begins.
  
−
We have the term stipule spine. Could also add the term '''stipule bristle''': A stipule that has a brush-like appearance.
+
proposed def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant begins.
  
−
A bristle is a single thing, like a stiff hair, but many things can be bristled. Better to add bristled as an adjective in PATO (like ovate or acute).
+
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
  
−
There are two meanings for bristled:  
+
Add related synonyms:
 +
* BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour
 +
* grape E-L stage: 35  Berries begin to colour and enlarge, beginning of veraison ''
  
−
!. Stiff and sharp (e.g., a bristled trichome)
+
* whole plant early fruit ripening stage (PO:0007001)
  
−
2. Bearing bristles (e.g, a bristled leaf bears many bristle-like hairs)
+
current name and def'n: FR.01 early stage of fruit ripening (PO:0007001): The early stage in fruit ripening
  
 +
proposed def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in an early stage.
  
−
Suggest two new phenotype descriptors (for PO phenotype branch or for PATO):
+
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
  
−
'''1. bristle-like:'''
+
Add related synonyms:
 +
* middle of veraison''
 +
*BBCH principal growth stage 83
  
−
This is a combination of two PATO descriptors:
+
'''* whole plant mid fruit ripening stage (PO:0007031):'''
 +
current name and def'n: FR.02 mid stage of fruit ripening (PO:0007031) The stage when fruit ripening is midway.
  
−
Something describing the shape:
+
proposed new def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is midway.
  
−
PATO:0001954 (subulate, awl-shaped, needle-shaped): A shape quality inhering in a bearer by virtue of the bearer's being linear, very narrow, tapering to a very fine point from a narrow base.
+
proposed comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
  
−
or
+
'''* whole plant late fruit ripening stage (PO:0007050):'''
  
−
PATO:0001873 (cylindrical): A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
+
current name and def'n: FR.03 late stage of fruit ripening (PO:0007050): The late stage of fruit ripening.
  
−
and/or PATO:0001154 (elongated): A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
+
proposed new def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in a late stage.
  
 +
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
  
−
and something describing a quality of a substance:
+
'''* whole plant fruit ripening complete stage (PO:0007038):'''
  
−
PATO has:
+
current name and def'n: FR.04 fruit ripening complete stage (PO:0007038): The stage at which fruit ripening is complete.
  
−
PATO:0001544 (flexible): A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. (bendy)
+
Proposed Def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of most of the fruits on the plant is complete.
  
−
PATO:0001545 (inflexibile): A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. (stiff)
+
comment: This term is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
  
−
A bristle is stiff but also bendy! I think in addition to flexible/inflexible, PATO needs terms for stiff or rigid/flacid, and that stiff should be a related synonym of inflexible, rather than exact.
+
related synonyms:
 +
* BBCH principal growth stage 89
 +
* grape E-L stage: 38;  Berries ripe for harvest
  
−
PATO:
+
=GO requests:=
  
−
quality of a substance (existing)
+
==[https://sourceforge.net/p/geneontology/ontology-requests/9075 Multicellular organism senescence/aging (GO:0010259)]==
  
−
>flexibility (existing)
+
* Multicellular organism senescence/aging (GO:0010259): includes loss of functions such as resistance to disease, homeostasis, and fertility, as well processes like cellular senescence, organ senescence, and wear and tear. The POC curators have requested to the GOC that they revise the definition of GO:0010259, to make it more appropriate for plants.
  
−
>>flexible (existing)
 
  
−
>>inflexible (existing)
+
Link to PO tracker: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/392/ gametophyte/sporophyte senescent stage]
  
−
>rigidity (new)
 
  
−
>>rigid (new)
+
''PJ Suggested revisions to leaf shaping (GO:0010358); Proposed new name: multidimensional leaf expansion: The developmental process that pertains to the organization of a leaf in three-dimensional space once the structure has initially formed. ''
  
−
>>flacid (new)
+
==apoplast and symplast==
 +
* apoplast (GO:0048046): The cell membranes and intracellular regions in a plant are connected through plasmodesmata, and plants may be described as having two major compartments: the living symplast and the non-living apoplast. The apoplast is external to the plasma membrane and includes cell walls, intercellular spaces and the lumen of dead structures such as xylem vessels. Water and solutes pass freely through it.
  
 +
''includes tracheids''
  
−
'''2. bristle-bearing:''' A pilosity quality inhering in a bearer by virtue of the bearer's having structures that are bristle-like.
+
This definition needs to be modified to be similar to the one for symplast. Lots of this should go in the comment.
  
−
is_a pilosity (PATO:0000066: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.)
+
* symplast (GO:0055044): The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata.
  
−
Synonym: bristly (Beentje 2010: bearing stiff strong hairs or bristles).
+
- all the plasma connected, through plasmodesmata, transport through the cytoplasm
  
 +
See: Link to diagram Apoplast_and_symplast_pathways
  
−
To describe legume stipules, we may also need a term '''brush-like:''' A shape quality inhering in a bearer by virtue of the bearer's having a shape that is a cluster of bristle-like structures.
+
See: Apoplastic versus Symplastic Pathways in roots
  
−
Then if we want to, we could add terms like '''brush-like stipule''' (is_a stipule) or '''bristle-like stipule''' (is_a stipule) or '''bristle-bearing stipule''', or users could post-compose these terms on their own.
+
* Suggest revised GO definitions for apoplast and symplast and add transport terms  
  
 +
Parent term:
  
−
=New Annotation Files=
+
* transport (GO:0006810): The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
  
−
===Strawberry===
+
* apoplastic transport (new GO term): A transport process (GO:id) that occurs in the apoplast (GO:0048046)
  
−
* Strawberry is on SVN: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_fragaria_jaiswallab.assoc?view=log strawberry]
+
* symplastic transport (new GO term): A transport process (GO:id) that occurs in the symplast (GO:0055044)
  
−
===Potato Annotations===
+
comments: symplastic transport is a diffusion process
  
−
LC has been in contact with the group who published the [http://www.nature.com/nature/journal/v475/n7355/full/nature10158.html#/f4 potato genome paper] and they are interested in collaborating with us to assign ontology terms to the annotations.
+
* Submit tracker for GO biol process term to describe callus formation
  
−
From Dr. Richard Finker (Wageningen, The Netherlands):  
+
=Wood ontology terms=
 +
See separate page: [[Wood Ontology PO and GO Term Development]]
  
−
"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."
+
=[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]=
  
−
''This will go in the next release, do they have expression data- RNA Seq?''
+
Submitted by Rich Zobel (Nov 2009).  Still need to work on definitions for these terms.
  
−
=Annotation Guidelines=
+
=Growth forms=
 +
From Daniel Hiss: "IMHO plant growth/life forms should be best integrated as an extension to PO."  Also need acrocarpous and pleurocarpous moss (these could be growth forms).
  
−
Comments from PJ from previous meeting (9-27-11):  
+
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3609139&group_id=36855&atid=440764 epidermis/epidermal cell : plant v. animal]==
−
Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids  methods and cut-offs, a guide for other collaborators and  a page for the info.
 
−
Maybe co-author it with SR
 
−
 
 
−
-This will also be helpful when applying for new grants
 
−
 
 
−
-it would be helpful to have a detailed guide on our wiki for collaborators
 

Latest revision as of 20:26, 17 July 2014

This page is a place holder for us to put items that are being worked on or under development.

Please include the date when the item was added; topics will move off of here as they are dealt with.

- Go back to POC_Meetings_Minutes main page

- All new terms and changes should be listed here: Release_21



Annotation Guidelines

Comments from PJ from previous meeting (9-27-11): Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR

-This will also be helpful when applying for new grants

-it would be helpful to have a detailed guide on our wiki for collaborators

Requests from SF- Anatomy terms in progress...

Request for "rind" or outer layer of a maize or sorghum stem

Request for a term for the outer covering of a maize or sorghum stalk.

link to #596

structure and properties of sorghum stalks


Propsed new terms:

Abscission Zones

June 2014

Added new terms and revised existing:

Ref: http://www.plantphysiol.org/content/158/1/439 (PMID:22106095)

See also:

  • Mao et al., Nature, 2000. JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development

(http://www.nature.com/nature/journal/v406/n6798/full/406910a0.html)

New term needed: flower pedicel abscission zone (PO:0025608)

flower pedicel abscission zone (PO:0025608): An abscission zone (PO:0000146) that forms as a swelling or joint on the flower pedicel (PO:009052).

PMID:24744429 Nakano T, et al. (2014) The AP2/ERF transcription factor SlERF52 functions in flower pedicel abscission in tomato. Journal of Experimental Botany.

http://jxb.oxfordjournals.org/content/early/2014/04/15/jxb.eru154.full

Added relations:

  • flower pedicel abscission zone (PO:0025608) part_of flower pedicel
  • fruit pedicel (PO:0004536) develops_from flower pedicel (PO:0009052)
  • fruit pedicel abscission zone (PO:0025605) develops_from flower pedicel abscission zone (PO:0025608)

Renamed existing term: pedicel > flower pedicel (PO:0009052)

Currently: pedicel (PO:0009052): An inflorescence branch (PO:0009081) that supports an individual flower (PO:0009046) in an inflorescence (PO:0009049).

Renamed: "flower pedicel" to differentiate it from the fruit pedicel (PO:0004536), which is an infructescence branch.

Renamed existing term: flower abscission zone > floral organ abscission zone (PO:0006502)

flower abscission zone (PO:0006502):

Was: Zone at base of the flower that contains an abscission (or separation) layer and a protective layer, both involved in the abscission of the flower and its parts.

This was revised as the AZ of a whole flower is different that that of the floral organs (sepals, petals and filaments).

Revised name and definition:

  • floral organ abscission zone (PO:0006502): An abscission zone (PO:0000146) at the base of a flower (PO:0009001) where a floral organ (PO:0025395) separates during floral organ abscission (GO:0010227).

Made this part_of a floral organ (PO:0025395), rather than a direct part_of a flower

New term request: microgametophtye development stage

Issue: We have megagametophyte development stage (PO:0007621), but do not have a similar term for microgametophtye development stage.

Question: how do the megagametophyte development stage (PO:0007621) and proposed microgametophtye development stage (new) fit in with the gametophyte development stage (PO:0028003)??

- multicellular plant gametangium (PO:0025124)- a plant organ- children: antheridium (PO:0025125) and archegonium (PO:0025126)

- unicellular plant gametangium (PO:0025521): a plant cell- no child terms...

Currently, megagametophyte development stage (PO:0007621) is_a ovule development stage (PO:0007619), but it should be part_of.

  • plant ovule (PO:0020003): A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006).
  • Moved megagametophyte development stage (PO:0007621) to be is_a gametophyte development stage (PO:0028003). part_of ovule development
    • Revised definition: A gametophyte development stage (PO:0028003) during which the megagametophyte (PO:0025279) develops.added dbxref to: OBO_SF2_PO: 589

This definition should be worked on further, and the child terms need work as well.

  • Created new term: microgametophtye development stage (PO:0025602): A gametophyte development stage (PO:0028003) during which a microgametophyte (PO:0025280) develops.
  • pollen development stage (PO:0001007) should be a is_a microgametophtye development stage since pollen is_a microgametophyte (PO:0025280).

Currently pollen development stage (PO:0001007) is_a androecium development stage (PO:0007605)- but it should probably be part_of.

androecium (PO:0009061): A collective phyllome structure (PO:0025023) composed all of the stamens (PO:0009029) in a flower (PO:0009046).


  • moved pollen development stage (PO:0001007) to be is_a child of the new term: microgametophtye development stage (PO:0025602). part of androecium development stage_ (PO:0007605)

Current definition: Stages of development of the pollen defined by characteristic morphological, cytological, histological or other visible features.

Revised definition: pollen development stage (PO:0001007): A microgametophtye development stage (PO:0025602) during which the pollen (PO:0025281) develops.

This definition should be worked on further, and the child terms need work as well.

caryopsis hull (PO:0006000)

  • caryopsis hull (PO:0006000): A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) and develops from a dried lemma and palea. [source: POC:Ramona_Walls]
    • Comment: None

I think in maize, the hull is actually pericarp tissue, perhaps we should not include the last part.

founder cells

New terms: phyllome founder cell (PO:0025586)]: A plant cell (PO:0009002) that is part of the phyllome anlagen (PO:0025430).

Comment: As a group, the phyllome founder cells encompass several layers of the shoot apical meristem (PO:0020148) and form a phyllome anlagen (PO:0025430). Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria.

PMID:12610522

vascular leaf founder cell (PO:0025592): A phyllome founder cell (PO:0025586) that is part of a vascular leaf anlagen (PO:0025431).

Comment: As a group, the vascular leaf founder cells encompass several layers of the shoot apical meristem (PO:0020148) and form a vascular leaf anlagen (PO:0025431). Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria.

Revised: vascular leaf anlagen formation stage PO:0001003: A vascular leaf initiation stage (PO:0007040) during which the vascular leaf founder cells (PO:0025592) of the shoot apical meristem (PO:0020148) form a vascular leaf anlagen (PO:0025431).

Revisions to cortex (PO:0005708) and other portion of ground tissue (PO:0025059) children

See notes from discussion on POC call POC_Conf._Call_9-24-13

Issue is that some cortex terms are children of cortex (PO:0005708) and others are is_a portion of ground tissue (PO:0025059)

Cortex terms.png


Fill in details here.....


New terms Added in Release #20:

  • fused perianth (new PO:0025880): A perianth (PO:0009058) in which one or more of the petals (PO:0009032), sepals (PO:0009031), and/or tepals (PO:0009033) are fused.

Comment: The petals (PO:0009032), sepals (PO:0009031) and tepals (PO:0009033) may be fused anywhere along the phyllome margin (PO:0025018). In some cases where the calyx (PO:0009060) and corolla (PO:0009060) are fused at the base it is referred to as a perianth tube.

-Added Narrow synonyms: adnate perianth and connate perianth

  • fused petal (new PO:0025583): - A petal (PO:0009032) that is part of a fused corolla (PO:0025581) or a fused perianth (PO:0025580).
    • Comment: In fused perianth (PO:0025580), the fused petal (PO:0025583) may be joined to a fused sepal (PO:0025584) or another fused petal.
  • free petal (PO:0025569): A petal (PO:0009032) that is part of a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).
      • comment: A free petal (PO:0025569) only occurs in a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583). If you are describing a petal (PO:0009032) that is part of a perianth (PO:0009058) where none of the sepals (PO:0009031) and/or petals (PO:0009032) are fused, you should use petal.


  • free sepal (PO:0025587): A sepal (PO:0009031)that is part of a perianth (PO:0009058) that contains fused sepals (PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).
    • comment: A free sepal (PO:0025587) only occurs in a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583). If you are describing a sepal (PO:0009031) that is part of a perianth (PO:0009058) where none of the sepals (PO:0009031) and/or petals (PO:0009032) are fused, you should use sepal.

Need to look at these associated terms:

  • is_a:
    • PO:0025324 : banner petal [0]
    • PO:0025326 : keel petal [0]
  • part_of
    • PO:0025144 : petal apex [0]
    • PO:0025146 : petal base [0]
    • PO:0006041 : petal epidermis [0]
    • PO:0025008 : petal margin [0]
    • PO:0006069 : petal parenchyma [0]
    • PO:0025511 : petal spur [0]
    • PO:0025218 : petal stomatal complex [0]
    • PO:0000054 : petal vascular system [0]
    • PO:0025325 : wing petal [0]


For corolla:

  • part_of:
    • corolla spur PO:0025512: Def'n: A collective organ part structure (PO:0025269) that is a slender, hollow extension of a corolla and has as parts segments of two more fused petals.

- should be is_a fused corolla?

    • keel PO:0025327: A boat-shaped collective phyllome structure (PO:0025023) that consists of the two lowest petals (PO:0009032) of a papilionaceous corolla (PO:0009059). Comment: The two petals of the keel are often fused at the apex and free at the base. The keel projects toward the front of the flower. Found in the flowers of some Fabaceae.
    • PO:0009032 : petal [0]
  • fused corolla (PO:0025581): A corolla (PO:0009059) that is composed of fused petals (PO:0025583).
  • calyptra corolla (PO:0025330): A fused corolla (PO:0025581) that is composed of fused petals (PO:0025583). Very similar definitions

epicalyx

  • epicalyx (PO:00090630): A collective phyllome structure (PO:0025023) composed of two or more phyllomes immediately outside the calyx (PO:0009060). [source: POC:curators]

Do we need a new term for epicalyx bract? - What are the individual members of the epicalyx; they are bracts.

Existing term: flower bract (PO:0009034): A bract that subtends a perianth that is part of a flower. [source: POC:curators]

Add epicalyx bract as an exact synonym?, or make a new child of flower bract . Not every flower bract is part of an epicalyx

Example from MAG: In the Trocodondraceae, the perianth is completely lacking, but they have little bracts subtending the reproductive structure.

Decided that we needed to add a new term:

epicalyx bract (new PO:0025577): A flower bract (PO:0009034) that is part of the epicalyx (PO:0009063). It will be sibling to the existing terms lemma and palea.

arilloid and arillode and caruncle

There is an issue in OE with these that the exact synonyms are the same in Spanish, so it generates an error.this was resolved in Release #20

  • arilloid (PO:0019022): A cardinal part of multi-tissue plant structure (PO:0025498) that is a fleshy outgrowth of a seed (PO:0009010). [source: ISBN:9780881928501]

Comment: Often conspicuous and found on seeds with a hard testa that are dispersed by animals. There is some variation in how different sources define the subtypes of arilloids.

Synonyms narrow: arillode; exact: ariloide (Spanish)

  • arillode (PO:0025378): An arilloid that is an elaborate outgrowth of a seed at the micropyler end. [source: ISBN:9780881928501]

Comment: Generally larger than a caruncle and not hard.

Synonyms exact: ariloide (Spanish)

  • caruncle (PO:0020060): An arilloid that is an outgrowth of a seed next to the micropyle. [source: ISBN:9780881928501]

Comment: Often hard and generally smaller and less elaborate than a arillode.

Synonyms exact: carúncula (Spanish)

  • aril PO:0009090: An arilloid that is an outgrowth of a seed from a seed funicle. [source: ISBN:9780881928501]

Synonyms exact: arilo (Spanish) exact: 仮種皮 (Japanese)

Comment : Usually envelopes most of the seed and is fleshy. If the ovule is pressed against the funicle to form a raphe, it may appear that the aril is growing from the raphe.

floral node

suggested definition: A cardinal organ part of a shoot axis where one or more flower may arise

Parent/relationship: is_a shoot node (PO:0005004)

Submitted: Johnny Lloyd


inflorescence node: A shoot node that is part of an inflorescence axis and where a spikelet, flower, floret or inflorescence branch is attached. [source: GR:Pankaj_Jaiswal]. PO:0006325

spine petiole

Requested by DWS: spine petiole (new PO:id)- A petiole that is sclerified and persistent.

The petiole abscisses longitudinally and the blade withers.

See the photo and description on this page: "Spines From Modified Petioles"

adventitious branch

Definition: A shoot axis (PO:00025029) that develops in an unusual place

Parent/relationship: is_a shoot axis (PO:0025029), develops from an adventitious bud


adventitious shoot axis

shoot-borne root (PO:0000042)

synonym: adventitious root

Need to align these three with the shoot-borne root

  • adventitious root apical meristem ; PO:0006021
  • adventitious root epidermis ; PO:0006039
  • adventitious root nodule ; PO:0000040

leaf lamina PO:0020039

-fix typo in comment

  • Def'n: A phyllome lamina (PO:0025396) that is the part of a leaf (PO:0025034) exclusive of the petiole (PO:0020038) or leaf sheath (PO:0020104), if either is present.
  • Comment: A leaf lamina is usually dorsiventrally flattened, but may be flattened in a median plant (perpendicular to the axis) in the case of phyllodes (PO:0025335) or other ensiform leaves (PO:0025333). This term should not be used for leaves that are not laminar (flat), like round leaves in Allium or needle-like leaves in Pinus or some Proteaceae.

If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.


Ultimate Unit (UU)

Requested by: Corvez Adele Created: 2013-02-01

  • Ultimate units are last branching-orders inserted at extremities of lateral branching systems. Each unit can divide several times, they are mostly tridimensional and their last dichotomies form ultimate appendages.

Corvez et al., 2012

suggested parentage: Ultimate unit is_a cardinal organ part

moss capsule

need to open tracker for this: moss capsule

prothallial cell and prothallium

On the POC POC call (12-11-12), we identified that we needed to add this as part of the gymnosperm pollen.

prothallial cell (PO:0025533):

proposed def'n: A vegetative plant cell (PO:0009002) that develops from the division of the microspore (PO:0020048) and is part of the microgametophyte of vascular plants other than angiosperms.

should add the PO id for microgametophyte (PO:0025280) to the definition


For reference about prothallial cells in gymnosperms see:

Morphology of gymnosperms, by John M. Coulter and Charles J. Chamberlain. pages 2277-278 and 339-340.

Available online: Coulter + Chamberlain, 1910


Note: prothallium is a synonym for thallus (PO:0030027) and ....

How does prothallial cell compare to microgametophyte vegetative cell?

prothallial cell (PO:0025533): current def'n: A vegetative plant cell (PO:0009002) that develops from the division of the microspore (PO:0020048) and is part of the microgametophyte of vascular plants other than angiosperms.

Revised: A native plant cell (PO:0025606) which is vegetative and develops from the division of the microspore (PO:0020048) of vascular plants other than angiosperms.

Revised comment: The prothallial cell (PO:0025533) is part of the microgametophyte (PO:0025280) and is believed to be the remnant of the vegetative tissue of the male gametophyte.

common primordium

This request was made by Elena Kramer during the beta review: , I wondered if there was some way to incorporate ...the phenomenon of common primordia (...would only apply to the development ontology)

"During floral development (at least in peas, maybe others), petals and stamens (and maybe other floral organs) may share a common primordium before development of a distinct petal or stamen primordia. We may want to add this to the flower developmental stage branch of the PGDSO."

This could be a structure in the PAE branch, and we can consider adding it as a stage when we work on flower development stages.

We all agreed that this should be a PAE, rather than a development stage. Need to propose definition on SF.

nucellar projections

The current definition of nucellar projection (PO:0008007) is: A portion of plant tissue that is the morphologically distinct portion of the nucellus overlying the vascular strands in the grass caryopsis. part_of nucellus.

This definition is specific to grasses, and should be rephrased, so it is more general.

Actually, I can't find any references to this outside grasses, so perhaps it is fine as is. Does anyone know of an example of this outside grasses? Maybe in other monocots?

No one know of an example outside grasses, so it is okay, but we can rephrase slightly to make it more braod.

proposed def.: A portion of plant tissue (PO:0009007) that is a morphologically distinct part of a nucellus (PO:0020020) overlying the vascular bundles (PO:0005020).

comment: Found a caryopsis in Poaceae.

part_of nucellus

rosette leaf and cauline leaf

The definitions for these terms need revision, especially cauline leaf. Rosette leaf is okay, but should be converted to genus-differentia form.

Current definitions:

rosette leaf (PO:0000014): One of multiple leaves borne in a rosette - a group of leaves, generally borne at the base of the plant, that are separated by very short internodes.

comment: Arabidopsis, vegetative development is characterized by the production of the rosette leaves.

cauline leaf (PO:0000013): Leaf or pairs/whorls of leaves borne on the stem. Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.

comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.


Perhaps we should use the appropriate growth stages in their definitions, e.g., PO:0007113 rosette growth, and PO:0007089 stem elongation. However, stem elongation is defined as a vegetative growth stage, so it doesn't really apply to plants that are bolting

proposed definitions

rosette leaf: A vascular leaf (PO:0009025) that is part of a collective leaf structure (PO:0025022) in which the leaves are borne on a stem base (PO:0008039) that has very short stem internodes (PO:0020142).

comment: In many species, including Arabidopsis thaliana, the sporophyte vegetative stage (PO:0007134) is characterized by the production of the rosette leaves.


cauline leaf (PO:0000013): A vascular leaf (PO:0009025) that is borne on a stem (PO:0009047) or branch (PO:0025073) that has elongated shoot internodes (PO:0005005).

comment: In species that undergo bolting, such as Arabidopsis thaliana, cauline leaves may start to develop before or after the shoot axes elongates.

Question: Are there ever cauline leaves forming on an inflorescence axis (PO:0020122)?


Links from Lol:

http://www.arabidopsis.org/portals/education/growth.jsp

http://www.jstor.org/stable/2656849

non-vascular rosette leaves?

At the POC meeting on 6/7/11, PJ suggested that we make new general terms for rosette leaf and cauline leaf, is_a children of leaf. Then we could make specific terms for vascular rosette leaf and vascular cauline leaf.

However, I don't know if the terms rosette leaf and cauline leaf are ever used for non-vascular plants. Certainly leaves occur on a stem in mosses and liverworts, but it is not the case that the leaves first form during a rosette stage then the stem elongates. Instead, leaves are formed from the stem apex as it elongates.

If rosette leaf and cauline leaf only have one child each (vascular rosette leaf or vascular cauline leaf), is there really a point in making the general category?

Don't need these

sporocyte

Existing definitions:

sporocyte (PO:0006204): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) spores.

microsporocyte (PO:0020047): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) microspores. [source: ISBN:0878934030]

synonyms: microspore mother cell, PMC, pollen mother cell

megasporocyte (PO:0000431): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores. [source: ISBN:0471245208]

synonyms: megaspore mother cell, MMC


At the POC meeting on 5/6/11, we agreed to add sporocyte develops_from archesporial cell.

Already have:

megasporocyte develops_from female archesporial cell

microsporocyte dvelops_from primary sporogenous cell, which develops_from male archesporial cell


Proposed definitions:

sporocyte (PO:0006204): A plant cell (PO:0009002) that develops from an archesporial cell (PO:0030056) and undergoes meiosis (GO:0007126) to produces four plant spores (PO:0025017).

Add: sporocyte develops_from archesporial cell

Should we add spore develops_from sporocyte? yes

meiosis (GO:0007126)


microsporocyte (PO:0020047): A sporocyte (PO:0006204) that develops from a primary sporogenous celll (PO:0006088) and undergoes meiosis (GO:0007126) to produces four microspores (PO:0020048). [source: ISBN:0878934030]

synonyms: microspore mother cell, PMC, pollen mother cell

Should we add microspore develops_from microsporocyte?

male meiosis (GO:0007140)

Better to use meiosis, rather than male meiosis.


megasporocyte (PO:0000431): A sporocyte (PO:0006204) that develops from a female archesporial cell (PO:0006015) and undergoes meiosis (GO:0007126) to produces four megaspores (PO:0020019). [source: ISBN:0471245208]

synonyms: megaspore mother cell, MMC

female meiosis (GO:0007143)

Better to use meiosis, rather than female meiosis.


Also need to address:

primary sporogenous cell (PO:0006088), current def.: It is formed by the division of the male archesporial initial. After several mitotic divisions these cells differentiate into pollen mother cells.


proposed def.: A plant cell (PO:0009002) that develops from a male archesporial cell (PO:0006014) and, after several mitotic divisions, develops into microsporocytes (PO:0020047).

okay


Note: external ontology ids should go in both the definition and as a Dbxref, because they don't work as links otherwise. They work as links okay in the comments.

spikelet

At the POC meeting on 8-30-11, we decided that this definition needs some work.

Current def.: Ultimate and congested inflorescence branch of the grasses. [source: APWeb:Glossary] Comment: It consists of one to many closely-packed flowers and associated glumes etc.

Should make it more general, because spikelets are found throughout the Poales (close relatives of grasses).


Proposed def.: A second order inflorescence that has as parts the glumes, a firinflorescence branches with short internodes, and a florets.

Comment: Part of a spike type inflorescence as found in grasses and other Poales.

From Ale:

spike: an unbranched, elongated inflorescence with sessile or subsessile flowers or spikelets maturing from the bottom upwards

spikelet: a small spike or secondary spike; the ultimate flower cluster of grasses and sedges, consisting of one to may flowers subtended by two bracts (glumes)

lamina areole

Propose new definitions:

phyllome lamina areole (PO:0025391): A cardinal organ part (PO:0025001) that is part of a phyllome lamina (PO:0025396) and is completely surrounded by phyllome lamina veins (PO:0025348) and cannot be divided into any smaller parts that are completely surrounded by phyllome lamina veins.

Comment: Any order of phyllome lamina vein can form the sides of a phyllome lamina areole. Taken together, the phyllome lamina areoles form a contiguous field of polygons over the area of a phyllome lamina. part_of phyllome lamina


leaf lamina areole (PO:0025392): A phyllome lamina areole (PO:0025391) that is part of a leaf lamina (PO:0020039) and is completely surrounded by leaf lamina veins (PO:0020138) and cannot be divided into any smaller parts that are completely surrounded by leaf lamina veins.

Comment: Any order of leaf lamina vein can form the sides of a leaf lamina areole. Taken together, the leaf lamina areoles form a contiguous field of polygons over the area of a leaf lamina. Free ending veinlets (PO:0025390) may be found within a leaf lamina areole. part_of leaf lamina

ovuliferous scale

New term to add, needed for definition of ovuliferous scale ovule (PO:0025491).

"Ovuliferous scale" seems to be the more commonly used name.

proposed def., ovuliferous scale: A megasporophyll (PO:0009027) that is part of a seed-scale complex (PO:id).

Comment: Has as part an ovuliferous scale ovule (PO:0025491) and is part of a ovulate cone ().

need to review this

Currently, ovuliferous scale is a narrow synonym of megasporophyll


ovulate cone, new term: A strobilus (PO:0025083) that has as parts ovuliferous scales () but no microsporophylls (PO:0009028).

synonym: female cone (related)

Move more specific synonyms form strobilus to these terms.

microsporangiate cone, new term: A strobilus (PO:0025083) that has as parts microsporophylls (PO:0009028) but no megasporophylls (PO:0009027).


seed-scale complex: A reproductive shoot system (PO:0025082) that is part of an ovulate cone (PO:0025083) and has as parts a ovuliferous scale () and a ovuliferous scale sterile bract ().


ovuliferous scale sterile bract: A bract (PO:0009055) that is part of a seed-scale complex and subtends an ovuliferous scale ().

Definitions of megasporophyll and microsporophyll

move part about angiosperms to the comment

Current def., megasporophyll: A structure upon which (or in the axil of which) one or more megasporangia are borne; in flowering plants, a carpel.

Current def., microporophyll: A structure on which one or more microsporangia are borne; in flowering plants, the stamen.

pericarp and seed coat

What is the problem with pericarp?

  • open tracker for pericarp cell types for PJ: "There are a number of pericarp components which may need PO terms".

see: http://www.relata.info/docs/RT%202008%201.pdf


pericarp (PO:0009084):A wall of a fruit, developed from the ovary or carpel wall.

Synonyms related: fruit peel, fruit rind

New def.: A portion of plant tissue that develops form the ovary wall and forms the outer layer or layers of a fruit.

comment: Usually has as parts an exocarp, mesocarp and endocarp. In a caryopsis, the pericarp is fused with the seed coat.

endocarp ; PO:0009086, synonym inner epidermis of pericarp

exocarp ; PO:0009085 synonyms outer epidermis of pericarp,


seed coat: A portion of plant tissue that is the covering of a seed derived from ovular - mainly integumentary - tissue.

Revised: A portion of plant tissue that develops from an integument and forms the covering of a seed. develops_from integument

Get rid of "usually" in def. of integument. From: http://en.wikipedia.org/wiki/Caryopsis

is a type of simple dry fruit — one that is monocarpelate (formed from a single carpel) and indehiscent (not opening at maturity) and resembles an achene, except that in a caryopsis the pericarp is fused with the thin seed coat.

The caryopsis is popularly called a grain and is the fruit typical of the family Poaceae (or Gramineae), such as wheat, rice, and corn.

The term grain is also used in a more general sense as synonymous with cereal (as in "cereal grains", which include some non-Gramineae). Considering that the fruit wall and the seed are intimately fused into a single unit, and the caryopsis or grain is a dry fruit, little concern is given to technically separating the terms "fruit" and "seed" in these plant structures. In many grains, the "hulls" to be separated before processing are actually flower bracts.

link to a more scientific source :http://www.jstor.org/stable/10.2307/2442251


we also have the term:

caryopsis hull (PO:0006000): A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) and develops from a dried lemma and palea. [source: POC:Ramona_Walls]

ovary and the like

An ovary is either the basal part of a carpel (in an apocarpous gyneocium) or the basal part of a syncarpous gynoecium. This is how it is defined in Esau, Raven, Weberling, etc.

The same can be said of a style or a stigma. Therefore, all of these can be either part_of carpel or part_of gynoecium (which means they are always part_of gynoecium).


ovary wall: Part_of ovary, which may be part of carpel or part of gyneocium. Not a valid COP.

style: (Raven: A slender column of tissue that arises from the top of an ovary and through which the pollen tube grows). Just like ovary, it may be part of a carpel or part of a group of fused carpels. Weberling uses "monocarpellary style" for a style of a single carpel and "polycarpellary style" for the style of fused carpels.

If the styles are fused at the base but free at the top, the free portions are called "style branches" or "stylodia" (Troll), or "stigma branches" if it is only the stigma portion that is free.

stigma: Raven defines this as a part of a carpel. Esau is ambiguous about how to treat stigma in syncarpous gynoecium. Weberling refers to a single stigma for fused carpels, but also to multiple stigmas, if the carpels are fused at the base and style, but then free at the tips, where the stigmas are. Also refers to stigma lobes (e.g., a tulip, with three fused carpels, has a single stigma, with three lobes. Seem like we have to treat stigma the same as ovary and style.

anther and filament

Weberling: Although filaments are often fused, they are still referred to as individual filaments (e.g., the corona of Narcissus consists of fused filaments (not a single filament), with the anthers inserted on the inner surface). Anthers may also fuse, but it is less common. He uses the term "synanther" of a single structure made of fused anthers (e.g., Gesneriaceae, see this cool picture).

It seems like it would be better to keep anther and filament as part of stamen, since that is the more commmon state. We can use special terminology for when they are fused (such as corona and synather).

Cacti terms:

spinule: word for when the spines are stipules – synonym of stipule spine

In Beentje, spinule is defined as a small spine.

Add "spinule" as narrow synonym for stipule spine and as related synonym for other kinds of spines.

cladode and phylloclade

From Beentje:

cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf

phylloclade: portion of stem or branch (several nodes and internodes) flattened and expanded to serve the functions of a leaf.

FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.

proposed definition:

cladode: A shoot axis that is flattened and expanded.

comment: Has an increased surface area for photosynthesis and may function similar to a leaf in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes.

synonyms: phylloclade, cladophyll

Dennis said: A shoot axis that is flattened. expanded is redundant. What about cholla? This does not work. The comment also does not work. Similarily the synonyms are not so much synonyms as they are subsets.

I don't know what the problem is with Cholla. As far as I know, it does not have cladodes or phylloclades, because the axes are round.

Recent interesting paper on cladodes in Asparagus:

Nakayama,H., Yamaguchi,T. and Tsukaya,H. (2012) Acquisition and Diversification of Cladodes: Leaf-Like Organs in the Genus Asparagus. The Plant Cell Online, 24, 929 –940.

PMID:22415273

In Asparagus, some cladodes have re-evolved a rounded shape. Are they still cladodes, or just shoot axes again at that point (given that the PO is not based on homology)?

rib

Should also add 'rib' for cacti and other plants.

Definition:

-caryopsis new child of fruit

-adventitious root nodule

Make two sub-types of tapetum

Based on the discussion on the PO conf call 4-9-13, we need to add the two types of tapetum(s). Added as a comment on tapetum for now.

See tracker at: tapetum types

Comment from DWS: there are two types of tapetum: ameboid and secretory/glandular:

Need to determine if it is more appropriate to put them as child of tapetum or anther wall tapetum.

See references in the literature to: Sporne KR (1973) A Note on the Evolutionary Status of Tapetal Types in Dicotyledons. New Phytologist 72: 1173–1174

link

link to book

link to OSU Thesis


Organizing the types of plant cells

New term added: native plant cell (PO:0025606) and moved all the non cultured types of cells there, but it really needs some organization.

In CL, they are organized by type:

  • absorptive cell CL:0000212 A cell that takes up and metabolizes substances.
  • ciliated cell ID: CL:0000064 A cell that has a filiform extrusion of the cell surface.
  • barrier cell ID: CL:0000215 A cell whose primary function is to prevent the transport of stuff across compartments.
  • defensive cell CL:0000473 A cell whose primary function is to protect the organism.
  • diploid cell ID: CL:0000415 A cell whose nucleus has two haploid genomes. xref_analog FMA:72300
  • haploid cell ID: CL:0000413 A cell whose nucleus contains a single haploid genome.
  • gamete ID: CL:0000300 A mature sexual reproductive cell having a single set of unpaired chromosomes.
  • polyploid cell ID: CL:0000412 A cell whose nucleus, or nuclei, each contain more than two haploid genomes.
  • secretory cell ID: CL:0000151 A cell that specializes in controlled release of one or more substances.
  • transporting cell ID: CL:0000627 A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances. xref_definition TAIR:sr
  • supportive cell ID: CL:0000630 A cell whose primary function is to support other cell types.
  • somatic cell ID: CL:0002371 A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
  • stem cell CL:0000034 A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
  • storage cell ID: CL:0000629 A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose.
  • stuff accumulating cell ID: CL:0000325 A cell that is specialised to accumulate a particular substance(s).

Revisions to Plant Structure Development Stages:

POC 9-10-13: Add comment on how every stage can end in accidental death. Also mention something death being the canonical end point

Stages of Plant Embryo Development

Currently: in Version #20, Aug 2013:

Plant Embryo Dev Stages.png

Note: Not sure where the coleoptilar stage (PO:0001094) fits in- it has no letter code and apparently never has (at least in the last 4 years). The A zygotic stage term was removed sometime in 2011. Currently the heirarchy looks quite odd as starts with "B- proembryo stage"

-Removed the letters in the names and added preceded_by to order the stages. made coleoptilar stage (PO:0001094) a subclass of bilateral stage (PO:0004507).

Revisions June-July 2014:

Screen Shot 2014-07-14 at 2.33.52 PM.png

  • plant embryo development stage (PO:0007631): A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and one of the following:
    • the beginning of the seed germination stage (PO:0007057) in seed plants,
    • the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
    • formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes,


An issue with the current definition is that it excludes the cotyledonary and true leaf formation stages, no? Also, the seed germination stage (PO:0007057) is defined as starting with seed imbibition.



    • Comment: Succeeds a plant zygote stage (PO:0001097). The plant embryo development stage generally starts after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. No plant species undergoes all of the sub-stages listed here.

Sub-classes:

plant proembryo stage (PO:0001180)]

plant proembryo stage (PO:0001180): A plant embryo development stage (PO:0007631) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and the onset of the plant globular embryo stage (PO:0001185).

  • comment: The plant proembryo stage occurs prior to the differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)).


-

plant embryo globular stage (PO:0001185)

plant embryo globular stage (PO:0001185): A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry.

    • comment: During the plant globular embryo stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.

Comments from SF-RW: "We need a way to distinguish the end of the proembryo and the beginning of this stage. I think the end can be distinguished by bilaterality. I will have to do some research to see if there are differences in when a proembryo stage ends across land plants."

"According to Howell 1998, "Proembryo is the term given to describe the embryo up to the stage when the protoderm can be recognized, which is usually the globular stage." (reference?)

"Of course, the problem with this is that we define the protoderm as arising from an apical meristem, and that is not the case in the embryo. Seems like some authors refer to it as an epidermis and some as a protoderm at this stage. I am not an expert in this, but I think I feel more comfortable with calling it a protoderm rather than a fully developed epidermis. In that case, I suggest modifying the definition of protoderm, which I will post on isssue 125."

presumably, this is referring to: (https://sourceforge.net/p/obo/plant-ontology-po-term-requests/125/)


proposed definition RW:

  • plant embryo globular stage (PO:0001185): A plant embryo development stage (PO:0007631) that occurs during the interval between when a protoderm (PO:0006210) is first recognizable in a plant embryo (PO:0009009) and the onset of a plant embryo bilateral stage (PO:0004507).

New comment: During the plant embryo globular stage, a plant embryo proper (PO:0000001) increases in diameter through cell division but retains radial symmetry, and differentiation of the three main tissue systems (vascular system (PO:0000034), epidermis (PO:0005679), and the portion of ground tissue (PO:0025059)) begins. During a plant embryo bilateral stage, the embryo begins to develop bilateral symmetry. Preceded by a plant proembryo stage (PO:0001180).

Propose re-revised def'n LC:

  • plant embryo globular stage (PO:0001185): A plant embryo development stage (PO:0007631) that occurs during the interval between when a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry, with the concomitant formation of a protoderm (PO:0006210), and the onset of a plant embryo bilateral stage (PO:0004507).

comment: During the plant globular embryo stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.

I would avoid describing the plant embryo bilateral stage here as it is confusing to the user. Could also mention the development of the embryo hypophysis (PO:0020109).


Goldberg et al, 1994 Science: ""Two critical events must occur after the embryo proper forms: (i) regions along the longitudinal apical-basal axis must differentiate from each other and generate embryonic organ systems, and (ii) the three primordial tissue layers of the embryo need to be specified. Both of these events take place during the globular-heart transition phase (Fig. 2 and Table 1). The embryo proper has a spherical shape during the proembryo and globular stages (Fig. 2). The first visible cell differentiation events occur at the 16-cell stage when the protoderm, or outer cell layer of the embryo proper, is produced and the hypophysis forms at the top of the suspensor (Fig. 2). Subsequent cell differentiation events within the embryo proper result in the production of an inner procambium tissue layer and a middle layer of ground meristem cells (Fig. 2)."


Revised def'n LC:

plant embryo globular stage (PO:0001185): A plant embryo development stage (PO:0007631) that occurs during the interval between when a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry (with the concomitant formation of a protoderm (PO:0006210)), and the onset of a plant embryo bilateral stage (PO:0004507).


--

plant embryo bilateral stage (PO:0004507)

plant embryo bilateral stage (PO:0004507): was: Change from radial to bilateral symmetry takes place during this embryonic stage.

revised def'n: A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) develops bilateral symmetry.


RW: New proposed definition:

* plant embryo bilateral stage (PO:0004507): A plant embryo development stage (PO:0007631) that occurs during the interval between the transition from radial to bilateral symmetry in a plant embryo proper (PO:0000001) and the onset of a plant embryo expanding cotyledon stage (PO:0001078).

new comment: During a plant embryo expanding cotyledon stage, the embryo axis (PO:0019018) and embryo cotyledons (PO:0025470) begin to elongate. A plant embryo bilateral stage contains the stage commonly known as the heart stage. Preceded by a plant embryo globular stage (PO:0001185).

Ref: PMID:24784759


--




--

Suggested revisions from Dora Szakonyi (from 2012-06-27):

  • See Open SF tracker: #488 embryo development terms
  • At the moment B proembryo stage_PO:0001180 is a synonym for both 'eight-celled stage in Arabidopsis' and 'two-celled stage in Arabidopsis'. Maybe it would be good to introduce as child terms separately:

* B proembryo stage_PO:0001180 (= preglobular stage)

  1. two-celled stage in Arabidopsis
  2. four-celled stage in Arabidopsis (= quadrant stage)
  3. eight-celled stage in Arabidopsis (= octant stage)

* Similarly, for C globular stage_PO:0001185 new child terms:

  1. dermatogen stage in Arabidopsis (=16-cell stage)
  2. early-globular stage in Arabidopsis (32-cell stage)
  3. mid-globular stage in Arabidopsis
  4. late-globular stage in Arabidopsis

* For D bilateral stage_PO:0004507

  1. Transition stage in Arabidopsis (=triangular stage)
  2. early-heart stage in Arabidopsis
  3. mid-heart stage in Arabidopsis
  4. late-heart stage in Arabidopsis

* E expanded cotyledon stage_PO:0001078 Linear cotyledon stage embryo

  1. early-torpedo stage in Arabidopsis
  2. mid-torpedo stage in Arabidopsis
  3. late-torpedo stage in Arabidopsis
  4. Bent cotyledon stage (curled cotyledon stage/walking stick stage)

* F mature embryo stage_PO:0001081


Older trackers:

References:

Other "To do" items:

  • Next: start working on the fruit ripening stages, leaf and and tuber development stages- see below
  • Complete edits on prothallial cell and prothallium
  • Post list of phloem terms to tracker- what needs to be done on them?
  • follow up with French fern folks about terms for ferns - email inquiry, terms on tracker
  • reopen gametophyte and sporophyte?
  • Resolve the question about axis vs stem
  • Open tracker for new term for caryopsis, other types of fruit
  • look at spikelet rachilla (PO:0009080): The axis of the spikelet, above the glumes. is_a inflorescence branch (PO:0025111). needs to be revised. tracker?
  • spikelet needs to be revised
  • ovary wall should not be a cardinal organ part as ovary is not an organ See Items_for_future_meetings#ovary_and_the_like below.
  • pappus element should not be a COP, as a pappus is not an organ- collective organ part structure. Each pappus element is a part of some organ (although there is some debate about which organ it is part of), thus pappus element is a cardinal organ part. The pappus is a collection of pappus elements, and therefor a collective organ part structure. I think the classification is correct.
  • egg apparatus- should not be a COP, as it part_of embryo sac which is_a megagametophyte which is_a whole plant This was classified back when we were looser with putting things under COP. Need to propose an alternative classification. Maybe a portion of plant tissue?
  • there are a number of parts of fruit such as the fruit septum (PO:0025268), fruit locule, fruit valve that should have dual parentage- e.g. fruit septum is_a septum (is_a col. organ part structure) and should also be is_a cardinal part of a multi-tissue plant structure.
  • Need to revisit the AISO annotations of segmented images, as some of the protoxylem terms are not in the live version yet (will be in Release #20).
  • Need to work on the development of the gametophytes in moss Moss Physcomitrella patens Reproductive Organ Development, Plant Phys, 2013
  • Add PO:id for tapetum (PO:0025313) to comment on tapetum cell (PO:0025543)
  • need to fix: paraclade cortex PO:0004721: A portion of ground tissue that is part of a cortex and part of a paraclade. - change to 'primary inflorescence branch cortex'; add PO:Ids
  • Add preceded_by to the sub-classes of floral organ formation stage (PO:0025585):
  • Need to fix: spikelet rachilla: (PO:0009080): The axis of the spikelet, above the glumes. [source: POC:curators] - Should be an inflorescence branch (primary?), add PO:Ids
  • look at caruncle (PO:0020060) again- came up in the contest of the arillode and arilloid.
  • Add a comment on the top level term about how all PSDS's may be terminated before reaching senescence stage.
  • should we add a costa has part hydrome and leptome, they are not always there?
  • fix comment on receptacle- strawberry is an accessory fruit, post on tracker
  • need to revisit the portion of meristem tissue definition- about 2 dozen direct is_a children, many of which are actually determinate tissues such as the phyllome anlagen (PO:0025430) and child terms, the primordium, etc
  • Need to revisit shoot node (PO:0005004): A cardinal organ part of a shoot axis where one or more spikelet, flower, floret, branch, bud, or leaf may arise. Refer to the POC call 10-1-13 for more details.
  • Need to revise 'root epidermis (PO:0006036)' to match the shoot system epidermis PO:0006035 (see POC_Conf._Call_10-29-13)
  • Consider getting rid of apical meristem (PO:0020144)- it forces dual parentage on the two child terms- shoot apical meristem (PO:0020148) and root apical meristem (PO:0020147) and forms a loop/cycle.



whole plant flowering stage PO:0007016

  • Now that we have revived the flowering stages, we need to revisit the whole plant flowering stages:

whole plant flowering stage (PO:0007016): A sporophyte reproductive stage (PO:0007130) during which a flower (PO:0009046) on a whole plant (PO:0000003) is open.

This is incorrect as in many plants, pollination occurs before the flowers open, especially self-pollinated plants

  • child terms need to be revised and the synonyms need to be reviewed, compare synonyms and stages
    • PO:0007026 : FL.00 first flower(s) open stage [24,868]
    • PO:0007034 : FL.01 1/4 of flowers open stage
    • PO:0007053 : FL.02 1/2 of flowers open stage [0]
    • PO:0007052 : FL.03 3/4 of flowers open stage [0]
    • PO:0007024 : FL.04 end of flowering stage [2]

Why are there ~25,000 associations on the first one and none on the rest? They look like they are all from Zea Mays, and 1 from SGN.


fruit development stages (PO:0001002)

  • To avoid confusion, the whole plant fruit development stages (PO:0025500) were renamed in Release_19 to make it clear that they apply to whole plants.
  • The plant phenotype pilot project needs terms for grain (fruit) development stages such as milk stage (as synonym for more general term) and mature or dry stage.
  • We currently have terms for two sub-classes:
    • fruit formation stage PO:0025501 [145]
      • PO:0025503 : fruit initiation stage [0]
      • PO:0025505 : fruit size 10 to 30% stage [0]
      • PO:0025506 : fruit size 30 to 50% stage [0]
      • PO:0025507 : fruit size 50 to 70% stage [0]
      • PO:0025508 : fruit size 70% to final size stage [0]
      • PO:0025504 : fruit size up to 10% stage [0]
    • PO:0025502 : fruit ripening stage [118]

fruit ripening stage PO:0025502 and sub-classes

New terms are needed to describe the stages of ripening for individual fruits. Have a revised parent term; need the sub-classes.

fruit ripening stage: A fruit development stage (PO:0001002) during which a single fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).

Comment: Succeeds a fruit formation stage (PO:0025501). This stage is to be used for an individual fruit. Fruit ripening (GO:0009835) is defined as: an aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal. For the development stage of a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).


fruit ripening (GO:0009835): An aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal.

related synonyms: fruit maturation; fruit senescence

PO:0001170 : seed development stage [33916]

  • PO:0004506 : developing seed stage [10]
  • PO:0001040 : dry seed stage [19]
  • PO:0007633 : endosperm development stage [33495]
  • PO:0004505 : fertilized ovule stage [4]
  • PO:0025374 : seed dormant stage [23]
  • PO:0007632 : seed maturation stage [12]

plant organ development stage (PO:0025339) and child terms:

  • moved leaf development (PO:0001050) to be subclass of phyllome development stage, will be adding flower bract development (PO:new) see below.

Phyllome snap shot.jpg

Comment: Includes stages for the initiation, expansion, and senescence of a phyllome such as a leaf, lemma, or stamen.

reproductive shoot system development stage (PO:0025530)

  • Is_a: collective plant organ structure development stage (PO:0025338)
  • We need to build a hierarchy for the development of conifer cones- as they are also reproductive shoot systems
    • A conifer cone is a strobilus (PO:0025083): A reproductive shoot system consisting of a number of modified leaves (sporophylls) or ovule-bearing scales grouped terminally on a stem. [source: ISBN:0716710072, POC:curators]
      • Comment: May be simple or compound. Found in lycophytes such as Selaginella and Lycopodium, sphenophytes such as Equisetum, gymnosperms such as cycad, conifers, gnetophytes and the pollen producing structures of Gingko. The term cone is often used for strobili that are woody. Flowers are sometimes considered bisexual strobili. Some flowering plants such as Alnus have inflorescences called catkins that resemble strobili, but are not.
  • moss reproductive structures: these would both be children of plant organ development, as moss lacks a shoot system.
    • multicellular plant gametangium (PO:0025124):- antheridium (PO:0025125) and archegonium (PO:0025126)- produce the gametes
    • sporangium (PO:0025094): A plant organ in which spores are produced.


Need to look at the fern sporangia- that is the reproductive structure for those plants


  • This would parallel the two existing sub-classes:

inflorescence development stage (PO:0021004)and sub-classes

  • Currently this has two sub-classes:
    • PO:0021004 : inflorescence initiation stage [0]
    • PO:0007037 : inflorescence bifurcation stage [0]
  • Inflorescence development stage (PO:0001083):A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).
    • inflorescence initiation stage (PO:0021004): Stage of inflorescence development marked by the formation of the inflorescence meristem on a vegetative branch. [source: POC:Felipe_Zapata]
    • inflorescence bifurcation stage ( PO:0007037): Stage of inflorescence development marked by the formation of two, often equal-sized, inflorescence meristems from one inflorescence meristem. [source: POC:curators]

These need to be revised and additional stages need to be developed.

flower development stage:

This is mostly done- this reference might be helpful for the legume flowers and have annotations to add. Floral Development in Legumes: (Plant Physiol, March 2003, Vol. 131, pp. 911-926)

collective phyllome structure development stage (PO:0025578) and child terms

collective phyllome structure development stage (PO:0025578): A collective plant organ structure development stage (PO:0025338) that has as primary participant collective phyllome structure (PO:0025023).

  • Made these part_of floral organ differentiation stage (PO:0007600), need to work on the definitions....
    • androecium development stage (PO:0007605): A collective phyllome structure development stage (PO:0025578) that has as a primary participant an androecium (PO:0009061).
    • calyx development stage (PO:0007603):A collective phyllome structure development stage (PO:0025578) that has as a primary participant a calyx (PO:0009060).
    • corolla development stage (PO:0007604):A collective phyllome structure development stage (PO:0025578) that has as a primary participant a corolla (PO:0009059).
    • gynoecium development stage (PO:0007606): A collective phyllome structure development stage (PO:0025578) that has a primary participant a gynoecium (PO:0009062).

Collective phyllome snap shot.jpg

New term flower bract development stage (new po:id)

flower bract development stage (new po:id):

- will be parent to lemma development stage and palea development stage

  • lemma development stage (PO:0001047): A phyllome development stage (PO:0025579) that has as a primary participant a lemma (PO:0009037).
    • PO:0001055 : lemma primordia visible stage [1]
    • PO:0001056 : lemma differentiation and expansion stage [0]
    • PO:0001057 : fully expanded lemma stage [0]


  • palea development stage (PO:0001048): A phyllome development stage (PO:0025579) that has as a primary participant a palea (PO:0009038).
    • PO:0001058 : palea primordia visible stage [1]
    • PO:0001070 : palea differentiation and expansion stage [0]
    • PO:0001071 : fully expanded palea stage [0]

anther development stage (PO:0001004) and its child terms

  • anther development stage (PO:0001004): Stages of development of the anther defined by characteristic morphological, cytological, histological or other visible features.
  • Is_a androecium development stage (PO:0007605):
  • In Release #19, we renamed anther wall tapetum degeneration initiated stage (PO:0001032): An anther development stage during which degeneration of the anther wall tapetum (PO:0009071) is initiated, as the deposition on the surface of the microspore (PO:0020048) primexine proceeds.

Blackmore S, Wortley AH, Skvarla JJ, Rowley JR (2007) Pollen wall development in flowering plants. New Phytologist 174: 483–498

tuber growth and development stages

This item has been open on SF since 6/2009, How we work these in will depend on restructuring of PSDS

We will have to differentiate between the two sub-types of tuber (PO:0025522), as they will have different development:

  • tuber (PO:0025522): A plant axis (PO:0025004) that is radially enlarged. [source: POC:curators]
  • PO:0004543: shoot axis tuber [6]
  • PO:0025476: tuberous root tuber [0]

So the main classes could be under: is_a plant axis development stage (PO: new) is_a plant organ development stage (PO:0025339)


From Naama Menda: "I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).

Suggested stages:

  • tuber initiation
  • tuber growth
  • tuber maturation

Would these be the same for the two different types of tubers? Also need: tuber dormancy

  • sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
  • All the SGN annotations refer to potato, which is a subterranean tuber (PO:0004547)
    • part_of children:
      • PO:0025070 : subterranean tuber axillary bud meristem
      • PO:0025081 : subterranean tuber axillary shoot (exact synonym: tuber sprout)
      • PO:0025042 : subterranean tuber axillary vegetative bud (narrow synonym: potato eye)
      • PO:0025048 : subterranean tuber epidermis
      • PO:0025045 : subterranean tuber periderm
      • PO:0025038 : subterranean tuber storage parenchyma


Further info and references:

Potato Growth & Development

Tuber on a chip: differential gene expression during potato tuber development

Growth of the Potato Tuber

xylem developmental stages:

See discussions of primary xylem on POC_Conf._Call_6-11-13

Existing definitions:

* secondary xylem development stage (PO:0025427): A xylem development stage (PO:0025425) that has as primary participant a portion of secondary xylem (PO:0005848) tissue during the interval between the beginning of a cell division stage of secondary xylem (PO:0025463) and the death of the last living cell in the secondary xylem. [source: POC:wood_curators]

  • Need: primary xylem development stage (PO:new): A xylem development stage (PO:0025425) that has as primary participant a primary xylem (PO:0005849) tissue. needs to be expanded

whole plant development stages (PO:0007033)

  • sporophyte vegetative stage (PO:0007134):

child terms need to be revised:

    • plant embryo stage (PO:0007631)
    • 0 seed germination stage (PO:0007057)
    • coleoptile emergence stage (PO:0007045)
    • 1 main shoot growth stage (PO:0007112)
    • 2 formation of axillary shoot stage (PO:0007073)
    • seedling development stage (PO:0007131)

whole plant fruit ripening stage (PO:0007010)

  • whole plant fruit ripening stage: A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.

Comment: Succeeds a whole plant fruit formation stage (PO:0007042). This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit ripening stage (PO:0025502). Although individual fruits are undergoing fruit ripening (GO:0009835), which is a type of senescence, during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An iteroparous species generally will have only one fruit ripening stage in its life, while a semelparous species may have multiple fruit ripening stage in its life. A whole plant fruit ripening stage may be followed by a sporophyte senescent stage, as in case (1) or by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species and species that fruit multiple times during a growing season, a plant may have multiple fruit development stages without entering dormancy or senescence, as in case (3). In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the whole plant fruit formation stage (PO:0007042) has ended. In some plants, fruit may continue to ripen after the whole plant has entered a sporophyte dormant stage or sporophyte senescent stage and left the whole plant fruit ripening stage. Some plants may never enter a whole plant fruit ripening stage, because fruits only begin to ripen after the plant has entered a sporophyte dormant stage or sporophyte senescent stage. Although the use of synonyms like "10-dough stage in sorghum" properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant. 


 **Add link to this tracker from the whole plant fruit ripening stage (PO:0007010)**

See comments from BS from email:

  • On Wed, Sep 18, 2013

- A lot of this needs to go, I think:

- early, middle and late are okay, but then we need to define them non-circularly and if you want to keep whole plant f.r. complete stage' then you have to define it so that it differs from 'late ...'

WPFRS.png

Proposed Revisions to sub-classes:

Comment from RW: The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point. 

need to open tracker for this set:

* whole plant beginning of fruit ripening stage (PO:0007036):

current name and def'n:FR.00 beginning of fruit ripening stage (PO:0007036): The stage at which fruit maturation begins.

proposed def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant begins.

comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

Add related synonyms:

  • BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour
  • grape E-L stage: 35 Berries begin to colour and enlarge, beginning of veraison
  • whole plant early fruit ripening stage (PO:0007001)

current name and def'n: FR.01 early stage of fruit ripening (PO:0007001): The early stage in fruit ripening

proposed def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in an early stage.

comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

Add related synonyms:

  • middle of veraison
  • BBCH principal growth stage 83

* whole plant mid fruit ripening stage (PO:0007031): current name and def'n: FR.02 mid stage of fruit ripening (PO:0007031) The stage when fruit ripening is midway.

proposed new def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is midway.

proposed comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

* whole plant late fruit ripening stage (PO:0007050):

current name and def'n: FR.03 late stage of fruit ripening (PO:0007050): The late stage of fruit ripening.

proposed new def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in a late stage.

comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

* whole plant fruit ripening complete stage (PO:0007038):

current name and def'n: FR.04 fruit ripening complete stage (PO:0007038): The stage at which fruit ripening is complete.

Proposed Def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of most of the fruits on the plant is complete.

comment: This term is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

related synonyms:

  • BBCH principal growth stage 89
  • grape E-L stage: 38; Berries ripe for harvest

GO requests:

Multicellular organism senescence/aging (GO:0010259)

  • Multicellular organism senescence/aging (GO:0010259): includes loss of functions such as resistance to disease, homeostasis, and fertility, as well processes like cellular senescence, organ senescence, and wear and tear. The POC curators have requested to the GOC that they revise the definition of GO:0010259, to make it more appropriate for plants.


Link to PO tracker: gametophyte/sporophyte senescent stage


PJ Suggested revisions to leaf shaping (GO:0010358); Proposed new name: multidimensional leaf expansion: The developmental process that pertains to the organization of a leaf in three-dimensional space once the structure has initially formed.

apoplast and symplast

  • apoplast (GO:0048046): The cell membranes and intracellular regions in a plant are connected through plasmodesmata, and plants may be described as having two major compartments: the living symplast and the non-living apoplast. The apoplast is external to the plasma membrane and includes cell walls, intercellular spaces and the lumen of dead structures such as xylem vessels. Water and solutes pass freely through it.

includes tracheids

This definition needs to be modified to be similar to the one for symplast. Lots of this should go in the comment.

  • symplast (GO:0055044): The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata.

- all the plasma connected, through plasmodesmata, transport through the cytoplasm

See: Link to diagram Apoplast_and_symplast_pathways

See: Apoplastic versus Symplastic Pathways in roots

  • Suggest revised GO definitions for apoplast and symplast and add transport terms

Parent term:

  • transport (GO:0006810): The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
  • apoplastic transport (new GO term): A transport process (GO:id) that occurs in the apoplast (GO:0048046)
  • symplastic transport (new GO term): A transport process (GO:id) that occurs in the symplast (GO:0055044)

comments: symplastic transport is a diffusion process

  • Submit tracker for GO biol process term to describe callus formation

Wood ontology terms

See separate page: Wood Ontology PO and GO Term Development

root terms

Submitted by Rich Zobel (Nov 2009). Still need to work on definitions for these terms.

Growth forms

From Daniel Hiss: "IMHO plant growth/life forms should be best integrated as an extension to PO." Also need acrocarpous and pleurocarpous moss (these could be growth forms).

epidermis/epidermal cell : plant v. animal

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